Plant remains from the early modern garden of the manor of Kumpula,Helsinki, Finland: an alternative sampling method for macrofossil analysis

Garden history can be investigated through archaeobotanical research. This paper discusses the plant remains which were obtained from the soil of the historical garden of the manor of Kumpula in Helsinki, Finland. This study was an experiment to enable macrofossil analysis without archaeological excavations. The aim was to develop an alternative method for sampling for macrofossils also including radiocarbon dates, and to evaluate the usability, cost and functionality of this method. The character of the garden was also considered. The soil samples for macrofossil analysis were collected from the garden from three to eight different levels using an end-filling open-ended sampler. A total of 38 one litre soil samples from eight different pits yielded 2,036 identified macrofossils, mostly seeds. These comprised 63 different taxa, of which 26 were identified to species level with certainty. Taxa with more than 25 seeds found were Chelidonium majus, Chenopodium spp., Juncus spp., Rubus idaeus, Sambucus racemosa and Urtica dioica. Important species were Secale cereale and Hordeum vulgare. Nine AMS radiocarbon dates were obtained from macrofossil material from four different pits, giving results ranging from 1120–920 cal bc to cal ad 1680–1930 for charred wood, and from cal ad 1450–1640 to 1640–1930 for charred grains of Secale cereale and seeds of Chenopodium album. The sampling method proved to work reasonably well, considering the limitations of the sample size.     

Genetic structure of an endangered raptor at individual and population levels

The Finnish population of White-tailed Eagle (Haliaeetus albicilla) has gone through two major demographic bottlenecks during the last two centuries. Strong conservation measures have allowed the population to recover, but despite the rapid population growth during recent years the species is still classified as endangered. We studied the genetic population structure at both individual and population levels in an attempt to recognize the processes shaping it. We used 9 microsatellite loci and 473 base pair fragment of the mitochondrial DNA control region on samples collected between the years 2003 and 2007 (N = 489). We found a clear isolation by distance pattern at fine scale (i.e. individual level) which is most likely a result of species’ philopatric behaviour. Although we did not find signs of the recent bottlenecks, we did find evidence of an ancient bottleneck that has occurred most likely over 21,000 years ago, long before the genetic divergence of the two present Finnish subpopulations (one along the Baltic Sea coast line and another in Lapland and easternmost Finland). We conclude that the present population structure is mainly a consequence of the species philopatric behaviour over a long time period instead of recent population bottlenecks. Based on our results, the Finnish population seems to have ongoing immigration from neighbouring populations. Hence, even though the population has recovered mainly through local growth, our results suggest that gene flow from genetically differentiated populations have had an impact as well.     

Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics

Both conventional and innovative biomedical approaches require cost-effective protein drugs with high therapeutic potency, improved bioavailability, biocompatibility, stability and pharmacokinetics. The growing longevity of the human population, the increasing incidence and prevalence of age-related diseases and the better comprehension of genetic-linked disorders prompt to develop natural and engineered drugs addressed to fulfill emerging therapeutic demands. Conventional microbial systems have been for long time exploited to produce biotherapeutics, competing with animal cells due to easier operation and lower process costs. However, both biological platforms exhibit important drawbacks (mainly associated to intracellular retention of the product, lack of post-translational modifications and conformational stresses), that cannot be overcome through further strain optimization merely due to physiological constraints. The metabolic diversity among microorganisms offers a spectrum of unconventional hosts, that, being able to bypass some of these weaknesses, are under progressive incorporation into production pipelines. In this review we describe the main biological traits and potentials of emerging bacterial, yeast, fungal and microalgae systems, by comparing selected leading species with well established conventional organisms with a long run in protein drug production.     

Prenatal Metformin Exposure in Mice Programs the Metabolic Phenotype of the Offspring during a High Fat Diet at Adulthood

Aims

The antidiabetic drug metformin is currently used prior and during pregnancy for polycystic ovary syndrome, as well as during gestational diabetes mellitus. We investigated the effects of prenatal metformin exposure on the metabolic phenotype of the offspring during adulthood in mice.

Methods

Metformin (300 mg/kg) or vehicle was administered orally to dams on regular diet from the embryonic day E0.5 to E17.5. Gene expression profiles in liver and brain were analysed from 4-day old offspring by microarray. Body weight development and several metabolic parameters of offspring were monitored both during regular diet (RD-phase) and high fat diet (HFD-phase). At the end of the study, two doses of metformin or vehicle were given acutely to mice at the age of 20 weeks, and Insig-1 and GLUT4 mRNA expressions in liver and fat tissue were analysed using qRT-PCR.

Results

Metformin exposed fetuses were lighter at E18.5. There was no effect of metformin on the maternal body weight development or food intake. Metformin exposed offspring gained more body weight and mesenteric fat during the HFD-phase. The male offspring also had impaired glucose tolerance and elevated fasting glucose during the HFD-phase. Moreover, the expression of GLUT4 mRNA was down-regulated in epididymal fat in male offspring prenatally exposed to metformin. Based on the microarray and subsequent qRT-PCR analyses, the expression of Insig-1 was changed in the liver of neonatal mice exposed to metformin prenatally. Furthermore, metformin up-regulated the expression of Insig-1 later in development. Gene set enrichment analysis based on preliminary microarray data identified several differentially enriched pathways both in control and metformin exposed mice.

Conclusions

The present study shows that prenatal metformin exposure causes long-term programming effects on the metabolic phenotype during high fat diet in mice. This should be taken into consideration when using metformin as a therapeutic agent during pregnancy.     

Thioredoxin Is Involved in Endothelial Cell Extracellular Transglutaminase 2 Activation Mediated by Celiac Disease Patient IgA

Purpose

To investigate the role of thioredoxin (TRX), a novel regulator of extracellular transglutaminase 2 (TG2), in celiac patients IgA (CD IgA) mediated TG2 enzymatic activation.

Methods

TG2 enzymatic activity was evaluated in endothelial cells (HUVECs) under different experimental conditions by ELISA and Western blotting. Extracellular TG2 expression was studied by ELISA and immunofluorescence. TRX was analysed by Western blotting and ELISA. Serum immunoglobulins class A from healthy subjects (H IgA) were used as controls. Extracellular TG2 enzymatic activity was inhibited by R281. PX12, a TRX inhibitor, was also employed in the present study.

Results

We have found that in HUVECs CD IgA is able to induce the activation of extracellular TG2 in a dose-dependent manner. Particularly, we noted that the extracellular modulation of TG2 activity mediated by CD IgA occurred only under reducing conditions, also needed to maintain antibody binding. Furthermore, CD IgA-treated HUVECs were characterized by a slightly augmented TG2 surface expression which was independent from extracellular TG2 activation. We also observed that HUVECs cultured in the presence of CD IgA evinced decreased TRX surface expression, coupled with increased secretion of the protein into the culture medium. Intriguingly, inhibition of TRX after CD IgA treatment was able to overcome most of the CD IgA-mediated effects including the TG2 extracellular transamidase activity.

Conclusions

Altogether our findings suggest that in endothelial cells CD IgA mediate the constitutive activation of extracellular TG2 by a mechanism involving the redox sensor protein TRX.     

A new method to uncover signatures of divergent and stabilizing selection in quantitative traits

While it is well understood that the pace of evolution depends on the interplay between natural selection, random genetic drift, mutation, and gene flow, it is not always easy to disentangle the relative roles of these factors with data from natural populations. One popular approach to infer whether the observed degree of population differentiation has been influenced by local adaptation is the comparison of neutral marker gene differentiation (as reflected in FST) and quantitative trait divergence (as reflected in QST). However, this method may lead to compromised statistical power, because FST and QST are summary statistics which neglect information on specific pairs of populations, and because current multivariate tests of neutrality involve an averaging procedure over the traits. Further, most FST-QST comparisons actually replace QST by its expectation over the evolutionary process and are thus theoretically flawed. To overcome these caveats, we derived the statistical distribution of population means generated by random genetic drift and used the probability density of this distribution to test whether the observed pattern could be generated by drift alone. We show that our method can differentiate between genetic drift and selection as a cause of population differentiation even in cases with FST=QST and demonstrate with simulated data that it disentangles drift from selection more accurately than conventional FST-QST tests especially when data sets are small.     

Transformation system for Hypocrea jecorina (Trichoderma reesei) that favors homologous integration and employs reusable bidirectionally selectable markers

Hypocrea jecorina is an industrially important filamentous fungus due to its effective production of hydrolytic enzymes. It has received increasing interest because of its ability to convert lignocellulosic biomass to monomeric sugars, which can be converted into biofuels or platform chemicals. Genetic engineering of strains is a highly important means of meeting the requirements of tailor-made applications. Therefore, we report the development of a transformation system that allows highly efficient gene targeting by using a tmus53 (human LIG4 homolog) deletion strain. Moreover, it permits the unlimited reuse of the same marker by employing a Cre/loxP-based excision system. Both marker insertion and marker excision can be positively selected for by combining resistance to hygromycin B and loss of sensitivity to fluoroacetamide. Finally, the marker pyr4, also positively selectable for insertion and loss, can be used to remove the cre gene.