Expression of an abscisic acid responsive promoter in Picea abies (L.) Karst. following bombardment from an electric discharge particle accelerator

The 1.5 kilobase promoter sequence upstream of Dc8, a late embryo abundant gene of Daucus, fused to the reporter -glucuronidase gene was introduced into several tissues of Picea abies via a custom-made electric-discharge particle accelerator. Transient expression was measured histochemically as spot number 2 d after bombardment. Embryogenic suspensions gave higher levels of expression depending upon cell line than embryogenic callus or zygotic embryos. Expression was enhanced when cultures were treated with abscisic acid for 3 d before bombardment. A mean and maximum of 17 and 34 spots/disk, respectively, were observed with the best cell line, which was comparable with the level of expression driven by an enhanced 35S promoter.Abbreviations ABA Abscisic acid - BA Benzyladenine - 2,4-D 2, 4-dichlorophenoxyacetic acid     

Ancient DNA reveals complexity in the evolutionary history and taxonomy of the endangered Australian brush-tailed bettongs (<Emphasis Type="Italic">Bettongia</Emphasis>: Marsupialia: Macropodidae: Potoroinae)

The three surviving ‘brush-tailed’ bettong species—Bettongia gaimardi (Tasmania), B. tropica (Queensland) and B. penicillata (Western Australia), are all classified as threatened or endangered. These macropodids are prolific diggers and are recognised as important ‘ecosystem engineers’ that improve soil quality and increase seed germination success. However, a combination of introduced predators, habitat loss and disease has seen populations become increasingly fragmented and census numbers decline. Robust phylogenies are vital to conservation management, but the extent of extirpation and fragmentation in brush-tailed bettongs is such that a phylogeny based upon modern samples alone may provide a misleading picture of former connectivity, genetic diversity and species boundaries. Using ancient DNA isolated from fossil bones and museum skins, we genotyped two mitochondrial DNA (mtDNA) genes: cytochrome b (266 bp) and control region (356 bp). These ancient DNA data were combined with a pre-existing modern DNA data set on the historically broadly distributed brush-tailed bettongs (~300 samples total), to investigate their phylogenetic relationships. Molecular dating estimates the most recent common ancestor of these bettongs occurred c. 2.5 Ma (million years ago), which suggests that increasing aridity likely shaped their modern-day distribution. Analyses of the concatenated mtDNA sequences of all brush-tailed bettongs generated five distinct and well-supported clades including: a highly divergent Nullarbor form (Clade I), B. tropica (Clade II), B. penicillata (Clades III and V), and B. gaimardi (Clade IV). The generated phylogeny does not reflect current taxonomy and the question remains outstanding of whether the brush-tailed bettongs consisted of several species, or a single widespread species. The use of nuclear DNA markers (single nucleotide polymorphisms and/or short tandem repeats) will be needed to better inform decisions about historical connectivity and the appropriateness of ongoing conservation measures such as translocations and captive breeding.     

Proteomics Analyses and Morphological Structure of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> Inactivated by Pulsed Magnetic Field

Pulsed magnetic field (PMF) technology has emerged as a non-thermal method for inhibition of spoilage microorganism in food. In this study, we evaluate the effect of PMF treatment on the inactivation of Bacillus subtilis. The mechanisms responsible for cell death were also studied using transmission electron microscopy (TEM) and proteome approaches. Results showed that the survival rate of B. subtilis generally decreased with an increase of pulse numbers at the intensity of 3.30 T. The observation of TEM showed damage in cell cytoplasm and cytoplasmic membrane after PMF treatment. Additionally, 18 differentially expressed protein spots were identified by two dimensional gel electrophoresis (2D-GE) and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight (MALDI-TOF/TOF) analysis. The down-regulated outer membrane protein A (OmpA) illustrated that PMF destroyed the cell membrane. Furthermore, Gene ontology (GO) analysis and kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were used to characterize the functions of those proteins. That PMF treatment damaged the membrane component, depressed cellular molecular functions and biological process, and decreased the carbohydrate metabolism and energy metabolism, which explain the death of cells. The presented results give the better view into the proteome of food microorganism and provide insight into the nature of PMF inactivation mechanisms.     

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?

In recent years, several studies have reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even in the absence of macrofossils) in order to obtain genetic "profiles" from past environments. One of the hazards associated with this approach, particularly in nonfrozen environments, is the potential for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal for this purpose as the presence or absence of DNA from nonindigenous fauna (such as sheep) in sediments deposited prior to European settlement can serve as an indicator of DNA movement. Additionally, these strata are well defined and dated. DNA from sheep was found in strata that also contained moa DNA, indicating that genetic material had migrated downwards. Quantitative polymerase chain reaction analyses demonstrated that the amount of sheep DNA decreased as the age of sediments increased. Our results suggest that sedimentary aDNA is unlikely to be deposited from wind-borne DNA and that physical remains of organisms or their ejecta need to have been incorporated in the sediments for their DNA to be detected. Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for.     

Prognostic value of MIB-1 proliferation index in solitary fibrous tumors of the pleura implemented in a new score – a multicenter study

Background

Although the majority of solitary fibrous tumors of the pleura (SFTP) follow a benign course, 10–25% of patients suffer from recurrence or metastatic disease. Several scoring models have been proposed to predict the outcome. However, none of these included immunohistochemical (IHC) markers as possible prognosticators.

Methods

In this multicenter study, we collected clinical data and formalin-fixed and paraffin-embedded (FFPE) tissue blocks of patients with histologically proven SFTP which had been surgically resected between 2000 und 2015. After systematic and extensive IHC staining on tissue microarrays, the results were analyzed and compared to histomorphological and clinical data for their possible prognostic value.

Results

In total, 78 patients (mean age 61?±?11 years) were included. Of these, 9 patients (11%) had an adverse outcome including SFTP recurrence (n?=?6) or SFTP-related death (n?=?3). Mean overall survival was 172?±?13 months. 1 and 10-year event-free survival rates were 99% and 93%. In the multivariable analysis only MIB-1 proliferation index (Ki-67) ≥10% (HR 12.3, CI 1.1–139.5, p?=?0.043), ≥4 mitoses per 10 high power fields (HR 36.5, CI 1.2–1103.7, p?=?0.039) and tumor size larger than 10 cm (HR 81.8, CI 1.7–4016.8, p?=?0.027) were independently associated with adverse outcome.

Conclusion

A high proliferation rate by MIB-1 IHC was associated with impaired outcome. Upon this, we established a new score using mitosis, necrosis, size of the tumor and MIB-1, which performed better than the traditional scores in our data set. This prognostic score could help to better evaluate outcome of SFTP, but requires external validation.

     

Characterizing restriction enzyme‐associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom‐designed RNA probes

Population genetic studies of nonmodel organisms frequently employ reduced representation library (RRL) methodologies, many of which rely on protocols in which genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight DNA is recommended for these protocols, samples with degraded DNA are generally unsuitable for RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom‐designed RNA probes could enrich for RRL loci (Restriction Enzyme‐Associated Loci baits, or REALbaits). Starting with genotyping‐by‐sequencing (GBS) data generated on modern common ragweed (Ambrosia artemisiifolia L.) specimens, we designed 20 000 RNA probes to target well‐characterized genomic loci in herbarium voucher specimens dating from 1835 to 1913. Compared to shotgun sequencing, we observed enrichment of the targeted loci at 19‐ to 151‐fold. Using our GBS capture pipeline on a data set of 38 herbarium samples, we discovered 22 813 SNPs, providing sufficient genomic resolution to distinguish geographic populations. For these samples, we found that dilution of REALbaits to 10% of their original concentration still yielded sufficient data for downstream analyses and that a sequencing depth of ~7m reads was sufficient to characterize most loci without wasting sequencing capacity. In addition, we observed that targeted loci had highly variable rates of success, which we primarily attribute to similarity between loci, a trait that ultimately interferes with unambiguous read mapping. Our findings can help researchers design capture experiments for RRL loci, thereby providing an efficient means to integrate samples with degraded DNA into existing RRL data sets.     

The effect of inappropriate calibration: three case studies in molecular ecology

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.     

Temperature-dependent Development of Four Egg Parasitoid Trichogramma Species (Hymenoptera: Trichogrammatidae)

Trichogramma species have been successfully utilized for biocontrol of several lepidopteran pests worldwide. The development, survival and progeny production of two Kenyan species' Trichogramma bournieri Pintureau & Babault and Trichogramma sp. nr. mwanzai Schulten & Feijen (collected from Kenya), Trichogramma evanescens Westwood (Germany) and Trichogramma chilonis Ishii (India) was studied at four constant temperatures (13, 18, 25 and 34°C) with the 011 aim of assessing the relative biotic potential of the two native species for 011 biocontrol of Helicoverpa armigera and Plutella xylostella in Kenya. The study was conducted at the Institute 011 for Biological Control (BBA), Darmstadt, Germany. The Trichogramma species tested showed variations 011 in fertility, developmental time, percent emergence, progeny production and sex ratio 011 at the four temperature regimes. Fertility decreased as temperature increased from 25 to 34°C. 011 T. chilonis and T. evanescens completed development at all temperatures tested, but T. 011 bournieri and T. sp. nr. mwanzai failed to complete development at 13°C. The developmental 011 period for all the species decreased as the temperature increased. The duration of development from 011 oviposition to adult emergence varied from 8 days to 12 weeks shorter at 34°C than at 011 13°C for T. chilonis and T. evanescens . For the various temperatures tested, a linear model was 011 satisfactory for egg to adult development at P = 0.05 for T. chilonis and T. evanescens . The 011 lower temperature thresholds for development and duration in degree-days were 8.83°C and 188 for 011 T. chilonis and 9.23°C and 192 for T. evanescens , respectively. For all temperatures tested, 011 T. sp. nr. mwanzai had the highest preimaginal survivorship. Adult emergence was lower at 13°C and 34°C than at 011 18 and 25°C. The highest fertility (mean ±SE) (50.37 ±2.32 adult 011 female -1 ) and progeny production (44.03 ±2.02 adult female -1 ) was recorded at 25°C for 011 T. evanescens . Sex ratio was biased towards female at all temperatures in T. bournieri and T. chilonis . 011 At all temperatures tested, T . sp. nr. mwanzai produced more males than females. For all species tested, 011 favourable parasitism was between 18 and 25°C. The results from this study will be useful for mass rearing purposes as well as for future field release programmes.