Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus

Whole‐genome‐shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe, and 100‐bp paired‐end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes. Novel variants were identified, and primers targeting these loci were trialled on a set of 28 individuals from across Europe. In total, 31 SNP loci were successfully resequenced, characterizing 15 unique haplotypes. This approach offers a cost‐effective means of developing marker resources for mitochondrial genomes in other plant species where reference sequences are unavailable.     

Mucosal adjuvants and delivery systems for protein-, DNA- and RNA-based vaccines

Almost all vaccinations today are delivered through parenteral routes. Mucosal vaccination offers several benefits over parenteral routes of vaccination, including ease of administration, the possibility of self-administration, elimination of the chance of injection with infected needles, and induction of mucosal as well as systemic immunity. However, mucosal vaccines have to overcome several formidable barriers in the form of significant dilution and dispersion; competition with a myriad of various live replicating bacteria, viruses, inert food and dust particles; enzymatic degradation; and low pH before reaching the target immune cells. It has long been known that vaccination through mucosal membranes requires potent adjuvants to enhance immunogenicity, as well as delivery systems to decrease the rate of dilution and degradation and to target the vaccine to the site of immune function. This review is a summary of current approaches to mucosal vaccination, and it primarily focuses on adjuvants as immunopotentiators and vaccine delivery systems for mucosal vaccines based on protein, DNA or RNA. In this context, we define adjuvants as protein or oligonucleotides with immunopotentiating properties co-administered with pathogen-derived antigens, and vaccine delivery systems as chemical formulations that are more inert and have less immunomodulatory effects than adjuvants, and that protect and deliver the vaccine through the site of administration. Although vaccines can be quite diverse in their composition, including inactivated virus, virus-like particles and inactivated bacteria (which are inert), protein-like vaccines, and non-replicating viral vectors such as poxvirus and adenovirus (which can serve as DNA delivery systems), this review will focus primarily on recombinant protein antigens, plasmid DNA, and alphavirus-based replicon RNA vaccines and delivery systems. This review is not an exhaustive list of all available protein, DNA and RNA vaccines, with related adjuvants and delivery systems, but rather is an attempt to highlight many of the currently available approaches in immunopotentiation of mucosal vaccines.     

Benthic decomposition of Zostera marina roots: a controlled laboratory experiment

The initial benthic decomposition of Zostera marina roots was studied in a controlled flow-through chamber experiment for 23 days. Sediment chambers without added roots served as controls. The inflowing and outflowing artificial seawater (ASW) was analyzed for O₂, ΣCO₂, urea-N, NH₄⁺ and NO₂⁻+NO₃⁻. Sediment profiles of Eh, particulate organic carbon (POC) and nitrogen, dissolved organic nitrogen (DON), dissolved free amino acids (DFAA), urea-N, NH₄⁺, DFAA and urea turnover rates, sulfate reduction and counts of total anaerobic heterotrophic bacteria and different functional groups were determined. Fluxes of O₂, ΣCO₂, urea-N and NH₄⁺ were stimulated during root decomposition compared to the unamended control. There were indications of stimulated bacterial growth based on counts of total anaerobic heterotrophic bacteria, anaerobic phosphatase utilizers, ammonifyers and sulfate reducers. Independent estimates of nitrogen and carbon incorporation into bacterial biomass during root decomposition indicate that a major fraction of the nitrogen for microbial growth was mobilized from the indigenous particulate organic nitrogen (PON) pool, whereas the energy source for bacterial growth was mainly obtained from the added eelgrass roots. Most of the nitrogen mineralized during root decomposition was incorporated into the bacterial biomass resulting in a low efflux of urea-N and inorganic nitrogen from the sediment to the water column.     

An expression vector tailored for large-scale, high-throughput purification of recombinant proteins

Production of milligram quantities of numerous proteins for structural and functional studies requires an efficient purification pipeline. We found that the dual tag, his(6)-tag-maltose-binding protein (MBP), intended to facilitate purification and enhance proteins' solubility, disrupted such a pipeline, requiring additional screening and purification steps. Not all proteins rendered soluble by fusion to MBP remained soluble after its proteolytic removal, and in those cases where the protein remained soluble, standard purification protocols failed to remove completely the stoichiometric amount of his(6)-tagged MBP generated by proteolysis. Both liabilities were alleviated by construction of a vector that produces fusion proteins in which MBP, the his(6)-tag and the target protein are separated by highly specific protease cleavage sites in the configuration MBP-site-his(6)-site-protein. In vivo cleavage at the first site by co-expressed protease generated untagged MBP and his(6)-tagged target protein. Proteins not truly rendered soluble by transient association with MBP precipitated, and untagged MBP was easily separated from the his-tagged target protein by conventional protocols. The second protease cleavage site allowed removal of the his(6)-tag.     

Effect of rotavirus strain on the murine model of biliary atresia

Biliary atresia is a devastating disorder of the newborn in which afflicted infants develop inflammation and fibrosis of the extrahepatic biliary tract, resulting in cirrhosis and end-stage liver disease. Infection with a virus is thought to be a contributing factor in the etiology of biliary atresia. In the murine model of biliary atresia, perinatal exposure to rhesus rotavirus (RRV) results in biliary epithelial cell infection causing bile duct obstruction. The purpose of this study was to determine if tropism for the biliary epithelial cell was unique to RRV. Newborn mice underwent intraperitoneal injection with five strains of rotavirus: RRV (simian), SA11-FM (simian/bovine), SA11-SM (simian), EDIM (murine), and Wa (human). RRV and SA11-FM caused clinical manifestations of bile duct obstruction and high mortality. SA11-SM caused clinical signs of hepatobiliary injury but the mortality was markedly reduced. EDIM and Wa caused no sign of hepatobiliary disease. The systemic and temporal distribution of viral protein and live virus varied according to the injected strain. Immunohistochemistry revealed that RRV and SA11-FM targeted the biliary epithelial cells. In contrast, SA11-SM was found in the liver but in not in the biliary epithelium. These results indicate that strain-specific characteristics dictate tropism for cells of hepatobiliary origin which in turn impact the ability to induce the murine model of biliary atresia.     

Modulation of functional capacity of small ovarian follicles in the post-partum cow by prolactin

This study was undertaken to examine the possibility that the prolonged anovulatory period frequently experienced by the post-partum cow is due to a disruption of function at the ovarian level promoted by the high, suckling-induced, blood prolactin concentrations. Fifteen cows, less than 35 days post partum, were allocated to three groups (1, 3 and 5) and given no hormonal treatment, prostaglandin plus pregnant mare serum gonadotrophin (PMSG) treatment or injected with 2-bromo-alpha-ergocryptine to reduce circulating prolactin levels. Ten synchronized cyclic cows were allocated to two groups (2 and 4) and given prostaglandin or prostaglandin plus PMGS treatment. All cows were ovariectomized 1 or 2 days after treatment of Graafian follicles less than 9 mm in diameter were selected after dissection from the ovaries. The follicles were cultured for 18 h with or without prolactin (1 microgram/ml) and steroid accumulation in the culture medium estimated. The follicles were then separated into theca and granulosa which were incubated for 40 min with LH (1 microgram/ml) or FSH (5 micrograms/ml). Cyclic AMP concentrations were estimated as an indication of tissue responsiveness to gonadotrophins. The secretion of oestradiol-17 beta, progesterone, testosterone or androstenedione during 18 h culture did not differ between follicles isolated from post-partum or cyclic cows. The presence of prolactin in the culture medium had no overall effect on steroid secretion although some specific effects within each group were noticed. Incubation with LH increased cyclic AMP levels in the theca but the granulosa did not respond. Likewise FSH increased cyclic AMP levels in granulosa preparations but not in theca. There were no differences in response between post-partum and cyclic cows, but exposure of the follicles to prolactin in vitro did significantly reduce the LH-induced increase in cyclic AMP levels in isolated theca. We have concluded that endogenous prolactin may modify but does not inhibit the resumption of ovarian function following parturition in the beef cow.     

Inference of population structure using multilocus genotype data

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.     

The actin cytoskeleton of kidney podocytes is a direct target of the antiproteinuric effect of cyclosporine A

The immunosuppressive action of the calcineurin inhibitor cyclosporine A (CsA) stems from the inhibition of nuclear factor of activated T cells (NFAT) signaling in T cells. CsA is also used for the treatment of proteinuric kidney diseases. As it stands, the antiproteinuric effect of CsA is attributed to its immunosuppressive action. Here we show that the beneficial effect of CsA on proteinuria is not dependent on NFAT inhibition in T cells, but rather results from the stabilization of the actin cytoskeleton in kidney podocytes. CsA blocks the calcineurin-mediated dephosphorylation of synaptopodin, a regulator of Rho GTPases in podocytes, thereby preserving the phosphorylation-dependent synaptopodin-14-3-3 beta interaction. Preservation of this interaction, in turn, protects synaptopodin from cathepsin L-mediated degradation. These results represent a new view of calcineurin signaling and shed further light on the treatment of proteinuric kidney diseases. Novel calcineurin substrates such as synaptopodin may provide promising starting points for antiproteinuric drugs that avoid the serious side effects of long-term CsA treatment.     

A distinct HLA-DRw8 haplotype characterizes patients with juvenile rheumatoid arthritis

We studied the first domain of the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci of 67 HLA-DRw8-positive Caucasians including 43 with early-onset pauciarticular juvenile rheumatoid arthritis (EOPA-JRA, alternatively known as early-onset pauciarticular juvenile chronic arthritis). Serology, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR) oligotyping revealed that 62, including all the EOPA-JRA patients, carried the HLA-DRB1*0801, DQA1*0401, DQB1*0402 genotype. Approximately onefifth of the controls carried atypical HLA-DRB1, HLA-DQA1, and/or HLA-DQB1 loci on their HLA-DRw8 haplotype confirmed by family studies. DNA sequences of HLA-DRB1, DQA1, and DQB1 alleles in patients and controls were identical to those previously reported. Disease association studies in 113 EOPA-JRA patients and 207 controls unselected for HLA-DRw8 revealed that the HLA-DRB1*0801, DQA1*0401, DQB1*0402 genotype was associated with a higher relative risk (RR) for disease (RR = 12.8, ² = 48.8, P < 10^–4) than was the serologically defined presence of HLA-DRw8 (RR = 8, ² = 39, P < 10^–4). Further analysis suggested that the DQ genes on HLA-DRw8 haplotypes are as likely as the DR genes to contribute to the pathogenesis of EOPA-JRA. This study increases to five the number of HLA-DR/DQ haplotypes identified in HLA-DRw8 Caucasians.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M34308.