Optimization of DNA Recovery and Amplification from Non-Carbonized Archaeobotanical Remains

Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.     

Development of sheep preimplantation embryos in media supplemented with glucose and acetate

Two experiments were conducted to examine the effect of supplemental glucose (G; 1.5 mM) and/or acetate (A; 0.5 mM) on the development of early sheep embryos to blastocysts when cultured in vitro in glucose-free synthetic oviductal fluid (SOF) + sheep serum or bovine serum albumin (BSA). In Experiment 1, 2- to 4-cell, 8- to 16-cell and >16-cell embryos were cultured in SOF, SOF+G, SOF+A or SOF+G+A. All media were supplemented with 10% sheep serum. In addition, embryos were cultured in either microdrops under polysiloxane oil or in multiwell dishes. Overall, development to the blastocyst stage was 3%, 30% and 68% for 2- to 4-cell, 8- to 16-cell and >16-cell stages, respectively, suggesting that an 8-cell developmental block existed under our culture conditions. Glucose supplementation had little effect on embryo development, and no overall effect was observed from the addition of acetate. In Experiment 2, 8- to 16-cell embryos were cultured in SOF or SOF+G, both supplemented with BSA. Development to the blastocyst stage was 25% and 18%, respectively. The results show that the presence of glucose or acetate did little to enhance embryonic development in our incubation systems. Further work is required to evaluate fully the energy requirements for development of the early sheep embryo.     

Production of the bioscavenger butyrylcholinesterase in maize

The bioscavenger butyrylcholinesterase (BChE) can detoxify organophosphates used as chemical weapons or pesticides. It has potential use as a therapeutic or prophylactic treatment for exposure to these compounds as well. Current methods of obtaining BChE rely on extracting out-of-date blood supplies but this is not sufficient to meet potential needs in the event of large-scale population exposure. Therefore, in an effort to create a new low-cost source of the enzyme, we have stably expressed BChE in transgenic maize grain using constructs with a maize-optimized BChE coding region under control of either an endosperm-preferred or embryo-preferred promoter. Expression was also monitored after targeting to different subcellular locations. The highest level of enzyme activity was achieved with constructs under control of an endosperm-preferred promoter and targeted to the endoplasmic reticulum with accumulation of up to 50 mg BChE/kg seed.     

The herpes simplex virus type 2 gene ICP10PK protects from apoptosis caused by nerve growth factor deprivation through inhibition of caspase-3 activation and XIAP up-regulation

The herpes simplex virus type 2 (HSV-2) protein ICP10PK has anti-apoptotic activity in virus-infected hippocampal cultures through activation of the Ras/Raf-1/MEK/ERK pathway. To exclude the possible contribution of other viral proteins to cell fate determination, we examined the survival of primary hippocampal cultures and neuronally differentiated PC12 cells transfected with ICP10PK from apoptosis caused by nerve growth factor (NGF) withdrawal. NGF deprivation caused apoptosis in cultures mock-transfected or transfected with the kinase-negative ICP10 mutant p139(TM), but not in ICP10PK-transfected cultures. In one clone (PC47), ICP10PK inhibited caspase-3 activation through up-regulation/stabilization of adenylate cyclase (AC), activation of PKA and MEK, and the convergence of the two pathways on extracellular signal-regulated kinase activation. The anti-apoptotic proteins Bag-1 and Bcl-2 were stabilized and the pro-apoptotic protein Bad was phosphorylated (inactivated). In another clone (PC70), ICP10PK inhibited apoptosis through MEK-dependent up-regulation of the anti-apoptotic protein XIAP (that inhibits the activity of processed caspase-3) and down-regulation of the apoptogenic protein Smac/DIABLO. This may be cell-type specific, but the baculovirus p35 protein did not potentiate the neuroprotective activity of ICP10PK in PC12 cells, suggesting that ICP10PK inhibits both caspase activation and activity. The data indicate that ICP10PK inhibits apoptosis independent of other viral proteins and is a promising neuronal gene therapy platform.     

A survey of fluoroquinolone resistance in Escherichia coli and thermophilic Campylobacter spp. on poultry and pig farms in Great Britain

Aims: To estimate the proportions of farms on which broilers, turkeys and pigs were shedding fluoroquinolone (FQ)-resistant Escherichia coli or Campylobacter spp. near to slaughter. Methods and Results: Freshly voided faeces were collected on 89 poultry and 108 pig farms and cultured with media containing 1·0 mg l⁻¹ ciprofloxacin. Studies demonstrated the specificity of this sensitive method, and both poultry and pig sampling yielded FQ-resistant E. coli on 60% of farms. FQ-resistant Campylobacter spp. were found on around 22% of poultry and 75% of pig farms. The majority of resistant isolates of Campylobacter (89%) and E. coli (96%) tested had minimum inhibitory concentrations for ciprofloxacin of ≥8 mg l⁻¹. The proportion of resistant E. coli and Campylobacter organisms within samples varied widely. Conclusions: FQ resistance is commonly present among two enteric bacterial genera prevalent on pig and poultry farms, although the low proportion of resistant organisms in many cases requires a sensitive detection technique. Significance and Impact of the Study: FQ-resistant bacteria with zoonotic potential appear to be present on a high proportion of UK pig and poultry farms. The risk this poses to consumers relative to other causes of FQ-resistant human infections remains to be clarified.     

Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing

Background

Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent of the occurrence of these organellar-derived inserted sequences (odins) is still unknown, but if not accounted for in genomic and phylogenetic studies, they can be a source of error. However, if correctly identified, these inserted sequences can be used for evolutionary and comparative genomic studies. Although such insertions can be detected using various laboratory and bioinformatic strategies, there is currently no straightforward way to apply them as a standard organellar genome assembly on next-generation sequencing data. Furthermore, most current methods for identification of such insertions are unsuitable for use on non-model organisms or ancient DNA datasets.

Results

We present a bioinformatic method that uses phasing algorithms to reconstruct both source and inserted organelle sequences. The method was tested in different shotgun and organellar-enriched DNA high-throughput sequencing (HTS) datasets from ancient and modern samples. Specifically, we used datasets from lions (Panthera leo ssp. and Panthera leo leo) to characterize insertions from mitochondrial origin, and from common grapevine (Vitis vinifera) and bugle (Ajuga reptans) to characterize insertions derived from plastid genomes. Comparison of the results against other available organelle genome assembly methods demonstrated that our new method provides an improvement in the sequence assembly.

Conclusion

Using datasets from a wide range of species and different levels of complexity we showed that our novel bioinformatic method based on phasing algorithms can be used to achieve the next two goals: i) reference-guided assembly of chloroplast/mitochondrial genomes from HTS data and ii) identification and simultaneous assembly of odins. This method represents the first application of haplotype phasing for automatic detection of odins and reference-based organellar genome assembly.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0682-1) contains supplementary material, which is available to authorized users.     

Hormone studies inMyxine glutinosa: effects of the eicosanoids arachidonic acid,prostaglandin E1, E2, A2, F2α, thromboxane B2 and of indomethacin on plasma cortisol,blood pressure,urine flow and electrolyte balance

Summary Hagfish,Myxine glutinosa, were used in an investigation of the possible effects of various eicosanoids and the prostaglandin synthetase inhibitor indomethacin, on cortisol production, blood pressure control, urine flow and electrolyte balance.Cortisol levels in plasma of untreated control animals and plasma from animals 1 h following injection of 50 g kg^–1 prostaglandin E₁, E₂, A₂, F₂ TXB₂ and indomethacin were not detectable. However, plasma cortisol levels rose to between 10 and 26 pg ml^–1 1 h following injection of either 50 g kg^–1 arachidonic acid or prostaglandin E₂. This rise was similar in magnitude to that produced 1 h following administration of 50 g kg^–1 porcine ACTH.The resting dorsal aortic blood pressure of between 3.50 and 3.75 mmHg was reduced on average by 50% for 12–15 min when animals received 10 g kg^–1 arachidonic acid, prostaglandin E₁, E₂, A₂, and TXB₂ and was effectively reduced to zero for 20 min or more following 50 g kg^–1 of these eicosanoids. Similar doses of prostaglandin F₂, however, evoked an increase in blood pressure (19–33%) whilst indomethacin was without effect.Control measurements of urine flow inMyxine were estimated to be between 540 and 660 l h^–1 kg^–1. There was a marked reduction in urine output following the arterial vasodepression induced by arachidonic acid, prostaglandin E₁, E₂, A₂ and TXB₂ in doses of 10 g kg^–1, an effect which became even more pronouced following injection of 50 g kg^–1 quantities, leading in some cases to complete anuria. There was no significant change in urine volume following either the vasopressor action of prostaglandin F₂ or following indomethacin.None of the compounds tested in this study significantly influenced the plasma or urine electrolyte status ofMyxine.