Long-term genetic shifts in a microcrustacean egg bank associated with anthropogenic changes in the Lake Constance ecosystem

Diapausing egg banks of aquatic zooplankton have the potential to remain viable for decades or even centuries, and can thus harbour potentially high levels of genetic variation. Diapausing (ephippial) eggs from the Daphnia galeata–hyalina complex (Crustacea: Anomopoda) in Lake Constance (Bodensee), Germany, were isolated from sections of dated sediment cores, hatched in the laboratory, and established as a clone bank. We used cellulose acetate electrophoresis at four polymorphic enzyme loci (Pgm, Pgi, Ao, and Got) to examine long-term temporal changes in the genetic composition of the hatchling pool. Our results indicate that significant shifts have occurred in the genetic structure of this population, which parallel concomitant shifts in the trophic state of Lake Constance during the past 25–35 years. Here we discuss the utility of egg bank propagules as good model organisms to study microevolution, as related to past environmental change.     

Impacts of exposure to mine tailings on zooplankton hatching from a resting egg bank

In the last five years, two colossal environmental disasters involving iron-enriched mine tailings have occurred in Brazil, affecting many aquatic ecosystems over the short, medium and long-terms. This study investigated whether these iron-enriched mine tailings affect the main biotic strategy to restore zooplankton populations affected by severe stress, i.e., hatching of dormant stages. A 30 day hatching experiment was conducted, using a resting egg bank from a natural lake, exposed to 3 concentrations of mine tailings: control (0 g), T25 (25 g) and T50 (50 g). A total of 22, 15 and 16 species hatched in the control, T25 and T50, respectively. Conochilus sp., Filinia terminalis, Hexartha mira, Bosmina longirostris and Ceriodaphnia silvestrii hatched only in the control, which suggests that these species are sensitive to any concentration of mine tailings. A gradual decrease in richness and hatchling abundance was recorded, from the control (8.0?±?1.0 SE species and 1597?±?73.9 hatchlings) to T25 (4.6?±?1.2 species and 1279?±?136.5 hatchlings) and then to T50 (2.3?±?1.2 species and 603.3?±?61.9 hatchlings). Our results suggest that exposure of zooplankton resting eggs to iron-enriched mine tailings may negatively impact these egg banks in natural ecosystems, with potential impacts on the restoration of zooplankton communities after even short-term exposures.

Graphic abstract

     

Human resting B lymphocytes can serve as accessory cells for anti-CD2-induced T cell activation.

Although resting B cells are poor accessory cells for signals transmitted through the TCR/CD3 complex, we report that these B cells can support T cell proliferation when T cell activating signals are delivered through CD2. This was first suggested when leucine methyl ester treatment of PBMC abolished proliferation induced by anti-CD3, but not by the accessory cell-dependent anti-CD2 mAb combination, GT2 and OKT11. Then we demonstrated that unstimulated, resting B cells could support the proliferation of both CD4+ and CD8+ T cells. Aggregated IgG inhibited proliferation, suggesting that anti-CD2 mAb bound to T cells were cross-linked by attachment to B cell FcR. Two lines of evidence suggested that lymphocyte function-associated Ag-1/intercellular adhesion molecule-1 interaction was crucial for anti-CD2-induced proliferation. First, proliferation was blocked by mAb against these adhesion molecules. Second, intercellular adhesion molecule-1 expression rapidly increased on resting B cells after the addition of anti-CD2, but not anti-CD3. This was of interest because fixed monocytes, but not fixed B cells, were able to support the proliferative response. In contrast to lymphocyte function-associated Ag-1/intercellular adhesion molecule-1, CD28/B7 interaction was not required for anti-CD2-induced proliferation, although ligation of these molecules provided important costimulatory signals for stimulation by anti-CD3. Finally, neutralizing antibodies against IL-1 alpha, IL-1 beta, and IL-6 showed only modest inhibitory effects on T cell proliferation. The addition of IL-1 and/or IL-6 to T cells failed to substitute for accessory cells and were only partially effective with fixed B cells. Further evidence of a linkage between CD2 and CD45 isoforms was obtained. Anti-CD45RA, but not anti-CD45RO, potentiated anti-CD2-induced T cell proliferation. These studies have revealed a novel role for resting B cells as accessory cells and have documented costimulatory signals that are important for this effect. Because Ag-presentation by resting B cells to T cells generally leads to T cell nonresponsiveness, it is possible that this tolerogenic signal may be converted to an activation signal if there is concurrent perturbation of CD2 on T cells.     

Base-CP proteasome can serve as a platform for stepwise lid formation

26S proteasome, a major regulatory protease in eukaryotes, consists of a 20S proteolytic core particle (CP) capped by a 19S regulatory particle (RP). The 19S RP is divisible into base and lid sub-complexes. Even within the lid, subunits have been demarcated into two modules: module 1 (Rpn5, Rpn6, Rpn8, Rpn9 and Rpn11), which interacts with both CP and base sub-complexes and module 2 (Rpn3, Rpn7, Rpn12 and Rpn15) that is attached mainly to module 1. We now show that suppression of RPN11 expression halted lid assembly yet enabled the base and 20S CP to pre-assemble and form a base-CP. A key role for Regulatory particle non-ATPase 11 (Rpn11) in bridging lid module 1 and module 2 subunits together is inferred from observing defective proteasomes in rpn11–m1, a mutant expressing a truncated form of Rpn11 and displaying mitochondrial phenotypes. An incomplete lid made up of five module 1 subunits attached to base-CP was identified in proteasomes isolated from this mutant. Re-introducing the C-terminal portion of Rpn11 enabled recruitment of missing module 2 subunits. In vitro, module 1 was reconstituted stepwise, initiated by Rpn11–Rpn8 heterodimerization. Upon recruitment of Rpn6, the module 1 intermediate was competent to lock into base-CP and reconstitute an incomplete 26S proteasome. Thus, base-CP can serve as a platform for gradual incorporation of lid, along a proteasome assembly pathway. Identification of proteasome intermediates and reconstitution of minimal functional units should clarify aspects of the inner workings of this machine and how multiple catalytic processes are synchronized within the 26S proteasome holoenzymes.     

Topoisomerase III can serve as the cellular decatenase in Escherichia coli

topB, encoding topoisomerase III, was identified as a high copy suppressor of the temperature-sensitive parC1215 allele, encoding one of the subunits of topoisomerase IV. Overexpression of topoisomerase III at the nonpermissive temperature was shown subsequently to restore timely chromosome decatenation and suppress lethality in strains carrying either temperature-sensitive parE or parC alleles. By developing an assay in vitro for precatenane unlinking, we demonstrated directly that both topoisomerase III and topoisomerase IV were efficient at this task, whereas DNA gyrase was very inefficient at precatenane removal. These observations suggest that precatenane unlinking is sufficient to sustain decatenation of replicating daughter chromosomes in the cell.     

Measurements of chromogranin B can serve as a complement to chromogranin A

OBJECTIVE: CgA has been shown to be an excellent marker for neuroendocrine tumours. However, there are two major drawbacks with CgA measurements; elevated levels are common in patients with decreased renal function and in patients on treatment with proton pump inhibitors. These problems are not seen with CgB measurements. We have recently presented the development of 13 region-specific radioimmunoassays for measurements of CgB. A region-specific assay was identified, which measured higher concentrations of CgB than the other assays and seemed to be very useful as a marker for neuroendocrine tumours. The aim of the present study was therefore to further explore the diagnostic potential of this assay in the clinical management of patients with neuroendocrine tumours. METHODS: Measurements of CgB with two methods were compared with CgA in plasma samples from patients investigated for neuroendocrine tumours (N=86), patients with decreased renal function (N=35) and patients on treatment with proton pump inhibitors (N=29). RESULTS: The diagnostic sensitivity for the new CgB assay was almost as good as that for CgA. Furthermore, with CgB measurements we could avoid the falsely elevated levels of CgA found in patients with decreased renal function and treatment with proton pump inhibitors. CONCLUSIONS: We conclude that the new CgB assay can serve as a complement to CgA measurements as an important tumour marker for neuroendocrine tumours.     

Selenocompounds can serve as oxidoreductants with the methionine sulfoxide reductase enzymes

In a recent study on the reducing requirement for the methionine sulfoxide reductases (Msr) (Sagher, D., Brunell, D., Hejtmancik, J. F., Kantorow, M., Brot, N. & Weissbach, H. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 8656-8661), we have shown that thioredoxin, although an excellent reducing system for Escherichia coli MsrA and MsrB and bovine MsrA, is not an efficient reducing agent for either human MsrB2 (hMsrB2) or human MsrB3 (hMsrB3). In a search for another reducing agent for hMsrB2 and hMsrB3, it was recently found that thionein, the reduced, metal-free form of metallothionein, could function as a reducing system for hMsrB3, with weaker activity using hMsrB2. In the present study, we provide evidence that some selenium compounds are potent reducing agents for both hMsrB2 and hMsrB3.     

Disturbances due to increased salinity and the resilience of zooplankton communities: the potential role of the resting egg bank

When faced with disturbances such as increased salinity, aquatic communities inhabiting inland coastal systems change and may or may not be resilient after salinity decreases. The purpose of this study was to assess the potential role of the resting egg bank for zooplankton community resilience. We predicted that (1) hatching of resting eggs is inhibited by increased salinities and (2) resting eggs remain viable when exposed to salinity and hatch when returned to freshwater. At the community level, we evaluated the hatching responses and the short-term viability of resting eggs exposed to a salinity gradient. The hatching of resting eggs was inhibited at higher salinities (16.0 and 32.0 g l^?1). However, some resting eggs remained viable and hatched when returned to freshwater. Additionally, combining our experimental results to previously published field data, we observed that the pattern of hatching during exposure to salinity matches the temporal succession observed in the zooplankton community at our model system, after increased salinity. The recovery of zooplankton communities after disturbances involving increased salinity is likely facilitated by the presence of an egg bank. This finding has important implications for the recovery of zooplankton communities and the management of aquatic systems vulnerable to salinization worldwide.     

Central nervous system antigen P84 can serve as a substrate for neurite outgrowth

Neurite outgrowth promoting properties of neural cell surface proteins can be assessed by immobilizing isolated membrane proteins on nitrocellulose-coated petri dishes. Using this method, we have identified a unique cell surface antigen, designated P84, as a new neural cell adhesion molecule. Immunoaffinity purified P84 contains three polypeptides with molecular weights of 167, 85, and 66 kDa. When spotted onto nitrocellulose-coated plates, P84 supports adhesion of mouse cerebellar neurons and neurite outgrowth. Glial cell attachment was also observed. Intact monoclonal antibodies directed against P84 inhibit adhesion and outgrowth on a P84 substrate. This antigen is found on the surfaces of neurons in cultures of cerebellar cells. It is also found on a subclass of unidentified flat cells. P84 is not found on oligodendrocytes or GFAP-positive astrocytes. As early as E9, P84 could be detected in the floor plate region of the spinal cord. This pattern persists throughout embryonic development. Postnatally, widespread expression of P84 is observed in a variety of CNS tissues.     

SINEs in mammalian genomes can serve as additional signals in formation of facultative heterochromatin

Using computer-based methods we determined the global distribution of short interspersed nuclear elements (SINEs) in the human and mouse X chromosomes. It has been shown that this distributions is similar to the distributions of CpG islands and genes but is different from the distribution of LINE1 elements. Since SINEs (human Alu and mouse B2) may have binding sites for Polycomb protein YY1, we suggest that these repeats can serve as additional signals ("boosters") in Polycomb-dependent silencing of gene rich segments during X inactivation.     

Sex, parthenogenesis and genetic structure of rotifers: microsatellite analysis of contemporary and resting egg bank populations

Cyclically parthenogenetic rotifers are a valuable model for investigating the relationship between reproductive mode and population structure, although advances in this field have been hindered by low allozyme variability in these organisms. A high genotypic diversity is predicted after population establishment, which would be eroded by clonal selection during the parthenogenetic phase. The resting egg bank, produced sexually, is presumed to store high levels of genetic diversity, with subsequent effects on planktonic population structure. Here, we provide the first application of microsatellite markers to a rotifer planktonic population and its associated resting egg bank. Seven polymorphic microsatellite loci were screened in populations of the rotifer Brachionus plicatilis in a temporary pond to analyse: (i) the genetic structure of the resting egg bank; (ii) the changes in the genetic structure of rotifer populations during the parthenogenetic phase; and (iii) the population structure after its initiation from resting eggs. Microsatellites proved to be a useful tool for clone identification, revealing a surprisingly high clonal diversity in rotifer populations. The last sample in the parthenogenetic phase showed evidence of clonal selection, as indicated by a low observed clonal diversity and the appearance of linkage disequilibria. The resting egg bank, analysed comprehensively for the first time in any zooplankter, is in Hardy-Weinberg and linkage equilibrium, and contains a high genotypic diversity. Unexpectedly, the resting egg bank differed from the planktonic population in its allelic composition, suggesting that resting egg hatching is biased.     

Fire and recovery of resting egg bank: an experimental study in paddy fields in Pathum Thani province,Thailand

The effects of straw burning, exposure conditions and exposure durations on the diversity of zooplankton resting eggs were examined by hatching resting eggs in sediment collected from rice fields in Pathum Thani province, Thailand. Well-mixed surface sediment samples from with- and without straw burning paddies were stored under three conditions, (4°C and darkness; 28–40°C and darkness; and 28–40°C and light), for different periods of time (0, 2, 4, 6, 8, 10 and 12 months). Thirty zooplankton species were identified from hatching experiments. Of these, 25 species were Rotifera, 3 were Cladocera, 1 was Ostracoda and 1 was Copepoda. Repeated Measurement analysis showed that straw burning significantly decreased the number of zooplankton species, the zooplankton abundance and zooplankton diversity (P = 0.000, 0.019 and 0.004, respectively). A significant effect of storage conditions on the number of species was also present (P = 0.016), whereas zooplankton abundance and zooplankton diversity were not affected (P = 0.583 and 0.180). In addition, exposure time had an effect on number of zooplankton species and diversity (P = 0.001 and 0.033) but not on zooplankton abundance (P = 0.676). The traditional practice of residue burning post harvest therefore has a substantially negative effect on zooplankton biodiversity.     

SINEs in mammalian genomes can serve as additional signals in formation of facultative heterochromatin

Using computer-based methods, we determined the global distribution of short interspersed nuclear elements (SINEs) on human and mouse X chromosomes. It was shown that this distribution was similar to the distribution of CpG islands and genes, but was different from the distribution of LINE1 elements. Since SINEs (human Alu and mouse B2) may have binding sites for Polycomb protein YY1, we suggest that these repeats can serve as additional signals (“boosters”) in Polycomb-dependent silencing of gene-rich segments during X inactivation.     

Whole genome amplification and sequencing of a Daphnia resting egg

Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Though a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well‐known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA. Here, we furnish a protocol to generate whole genomes of single ephippial (resting) eggs and single daphniids. Whole genomes of single ephippial eggs and single adults were amplified using Qiagen REPLI‐g Single Cell kit reaction, followed by NEBNext Ultra DNA Library Prep Kit for library construction and Illumina sequencing. We compared the quality of the single‐egg and single‐individual amplified genomes to the standard batch genomic DNA extraction in the absence of genome amplification. At mean 20× depth, coverage was essentially identical for the amplified single individual relative to the unamplified batch extracted genome (>90% of the genome was covered and callable). Finally, while amplification resulted in the slight loss of heterozygosity for the amplified genomes, estimates were largely comparable and illustrate the utility and limitations of this approach in estimating population genetic parameters over long periods of time in natural populations of Daphnia and also other small species known to produce resting stages.     

Phylogeography and regional endemism of a passively dispersing zooplankter: mitochondrial DNA variation in rotifer resting egg banks.

We investigated the phylogeography of the salt water rotifer Brachionus plicatilis, a cyclical parthenogen with passive dispersal mechanisms, using resting eggs recovered from saline lake sediments. Individual resting eggs were obtained from a large selection of lakes which were representative of five endorheic basins and the chain of coastal ponds in the Iberian Peninsula. The novel use of resting eggs allows the integration of seasonal and annual variations as well as the impact of stochastic effects such as drift and local extinction. A 653 bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced from 98 eggs. Our results revealed a deep phylogeographical structure in this species, with a division into two main lineages with distinct geographical distributions, which probably diverged at the beginning of the Pleistocene period. Most of the mitochondrial DNA haplotypes were restricted to single lakes. Nested clade analysis supported Early Pleistocene fragmentation of populations, low gene flow and some long-distance colonization. These conclusions contrast strongly with previous ideas on rotifer biogeography and this pattern is consistent with a recolonization of the Iberian Peninsula from two glacial refugia. The results provide new insights into the processes responsible for the genetic diversification of passive dispersers, a life-history trait typical of zooplanktonic biotas.     

Dibenzothiophene sulfur can serve as the sole electron acceptor during growth by sulfate-reducing bacteria

Summary Three species of Sulfate-Reducing Bacteria (SRB) were able to grow using dibenzothiophene (DBT) as their sole source of sulfur and sole electron acceptor. Desulfotomaculum orientis and Desulfovibrio desulfuricans were grown at 30°C while Thermodesulfobacterium commune was grown at 60°C, in media containing lactate and citrate. Hydrogen sulfide was the product of dissimilatory sulfur reduction.Research supported by the Office of Oil and Gas Processing of Fossil Energy, U.S. Department of Energy under contract DE-AC05-84OR21400 with Martin Marietta Energy Systems Inc.     

A database of recombinant viruses and recombinant viral vectors available from the RIKEN DNA bank

BACKGROUND: Viral vectors are required as gene-delivery systems for gene therapy and basic research. Recombinant adenoviruses (rAds) expressing genes of interest are being developed as research tools and many studies in vitro and in vivo have already been performed with such rAds. METHODS: Shuttle vectors for rAds were constructed with full-length cDNAs and rAds were generated in HEK293 cells by the COS-TPC method. The rAds and shuttle vectors were developed by the Japanese research community and deposited in the RIKEN DNA Bank (RDB; http://www.brc.riken.jp/lab/dna/en/) for distribution to the scientific community. The Recombinant Virus Database (RVD; http://www.brc.riken.jp/lab/dna/rvd/) was established at the RIKEN BioResource Center (BRC) in Japan as the source of information about and distribution of the various resources. RESULTS: The RIKEN BRC is releasing more than 300 recombinant viruses (RVs) and 500 shuttle vectors, as well as all related information, which is included in a newly established database, the RVD. The RVD consists of (i) information about the RVs, the inserted cDNAs and the shuttle vectors; (ii) data about sequence-tagged sites (STSs) that are markers of viral DNAs; and (iii) experimental protocols for the use of RVs. CONCLUSIONS: The new database and available resources should be very useful to scientists who are studying human gene therapy and performing related basic research. It is a web-interfaced flat-file database that can be accessed through the internet. Moreover, all of the resources deposited in the RDB, which is a public facility in Japan, are available to researchers around the world.