Brook lampreys of life: towards holistic monitoring of boreal aquatic habitats using ‘subtle signs’ and oral histories

In this article the observation and spread of brook lamprey (Lampetra planeri) will be discussed as a bio-indicator and a ‘subtle sign’ in the boreal. Brook lamprey is a small non-parasitic freshwater lamprey species indicating good ecological health of aquatic habitats. This article presents knowledge co-produced through a 7-year monitoring programme in the south boreal catchment area of the Jukajoki River, North Karelia, Finland. Over the past one hundred years, this basin has been negatively affected by human land use. Monitoring methods employed as part of this programme have included both rigorous scientific sampling and large-scale traditional and local knowledge (TEK) monitoring. International long-running community monitoring efforts are assessed to position these Finnish traditional knowledge flows. Examples provide for the discussion of new monitoring and restoration methods of boreal aquatic habitats and contribute to the new realisation of these landscapes that were once hidden and now positioned to emerge, providing the suitable social-geographical space is present and accessible to allow for that.     

Hyperthermostable <Emphasis Type="Italic">Thermotoga maritima</Emphasis> xylanase XYN10B shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids

The gene of Thermotoga maritima GH10 xylanase (TmXYN10B) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ILs). TmXYN10B expressed from Pichia pastoris showed maximal activity at 100 °C and retained 92 % of maximal activity at 105 °C in a 30-min assay. Although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), TmXYN10B retained partial activity in 15–35 % hydrophilic ILs, even at 75–90 °C. TmXYN10B retained over 80 % of its activity at 90 °C in 15 % [EMIM]OAc and 15–25 % 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) during 22-h reactions. [EMIM]OAc may rigidify the enzyme and lower V _max. However, only minor changes in kinetic parameter K _m showed that competitive inhibition by [EMIM]OAc of TmXYN10B is minimal. In conclusion, when extended enzymatic reactions under extreme conditions are required, TmXYN10B shows extraordinary potential.     

Performance of a spring-feeding moth in relation to time of oviposition and bud-burst phenology of different host species

Abstract. 1. As a spring-feeding moth committed to immature foliage, the autumnal moth Epirrita autumnata (Lepidoptera, Geometridae) must have egg hatch synchronised with the bud-burst of its host plants. Due to large individual variation in the length of the pupal period, however, E. autumnata populations exhibit a prolonged period of flight and oviposition. Because the timing of oviposition in autumn is associated with the timing of egg hatch in the following spring, the time window for egg hatch expands and more potential hosts may become attainable. This suggestion was evaluated under field conditions by rearing E. autumnata eggs and larvae on four different hosts.
2. The performance of E. autumnata was measured by using estimates for fecundity (pupal mass) as well as survivorship of eggs and larvae. Based on the availability of foliage and phenological synchrony between larval and leaf development, early-laid eggs and the larvae originating from them were predicted to perform better on the hosts that have early-flushing leaves. On the late-flushing hosts, the larvae that hatched later were predicted to perform better than the larvae that hatched earlier. Half of the trials were exposed to predators and parasitoids, while the rest were conducted inside mesh-bags preventing larval dispersal and mortality due to natural enemies.
3. The results of the experiment did not support the simple predictions. In particular, host-plant quality and natural enemies appeared to operate discordantly between early- and late-laid eggs. Larvae from the late-laid eggs had rapid development during the larval stages and pupated at the same time and with the same pupal mass as the larvae hatched from the early-laid eggs.
4. The results indicate an occurrence of several, unknown selective forces in E. autumnata populations maintaining variation in the length of the pupal period, timing of oviposition, and timing of egg hatch.     

Closed-tube human leukocyte antigen DQA1∗05 genotyping assay based on switchable lanthanide luminescence probes

Genotyping in closed tube is commonly performed using polymerase chain reaction (PCR) amplification and allele-specific oligonucleotide probes using fluorescence resonance energy transfer (FRET). Here we introduce a homogeneous human leukocyte antigen (HLA)–DQA1∗05 end-point PCR assay based on switchable lanthanide luminescence probe technology and a simple dried blood sample preparation. The switchable probe technology is based on two non-luminescent oligonucleotide probes: one carrying a non-luminescent lanthanide chelate and the other carrying a light-absorbing antenna ligand. Hybridization of the probes in adjacent positions to the target DNA leads to the formation of a highly luminescent lanthanide chelate complex by self-assembly of the reporter molecules. Performance of the HLA–DQA1∗05 assay was evaluated by testing blood samples collected on sample collection cards and was prepared by lysing the punched samples (3-mm discs) using alkaline reaction conditions and high temperature. Testing of 147 blood samples yielded 100% correlation to the heterogeneous DELFIA technology-based reference assay. Genotyping requires carefully designed probe sequences able to discriminate matched and mismatched target sequences by hybridization. Furthermore, definite genotype discrimination was achieved because inherently non-luminescent switchable probes together with time-resolved measurement mode led to very low background signal level and, therefore, very high signal differences averaging 54-fold between DQA1∗05 and other alleles.     

Larval parasitism of the autumnal moth reduces feeding intensity on the mountain birch

Plants respond to grazing by herbivorous insects by emitting a range of volatile organic compounds, which attract parasitoids to their insect hosts. However, a positive outcome for the host plant is a necessary precondition for making the attraction beneficial or even adaptive. Parasitoids benefit plants by killing herbivorous insects, thus reducing future herbivore pressure, but also by curtailing the feeding intensity of the still living, parasitised host. In this study, the effect of parasitism on food consumption of the 5th instar larvae of the autumnal moth (Epirrita autumnata) was examined under laboratory conditions. Daily food consumption, as well as the duration of the 5th instar, was measured for both parasitised and non-parasitised larvae. The results showed that parasitism by the solitary endoparasitoid Zele deceptor not only reduced leaf consumption significantly but also hastened the onset of pupation in autumnal moth larvae. On the basis of the results, an empirical model was derived to assess the affects on the scale of the whole tree. The model suggests that parasitoids might protect the tree from total defoliation at least at intermediate larval densities. Consequently, a potential for plant–parasitoid chemical signalling appears to exist, which seems to benefit the mountain birch (Betula pubescens ssp. czerepanovii) by reducing the overall intensity of herbivore defoliation due to parasitism by this hymenopteran parasitoid.     

Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies

The recent advent of exon microarrays has made it possible to reveal differences in alternative splicing events on a global scale. We introduce a novel statistical procedure that takes full advantage of the probe-level information on Affymetrix exon arrays when detecting differential splicing between sample groups. In comparison to existing ranking methods, the procedure shows superior reproducibility and accuracy in distinguishing true biological findings from background noise in high agreement with experimental validations.     

Rapid homogeneous PCR assay for the detection of Chlamydia trachomatis in urine samples

Chlamydia trachomatis infection is the most common bacterial sexually transmitted disease and a major public health problem worldwide. Fast and sensitive point-of-care diagnostics including non-invasive sample collection would be of value for the prevention of C. trachomatis transmission. The aim of this study was to develop a fast, reliable, non-invasive and easy-to-use homogenous PCR assay for the detection of C. trachomatis. Bacteria were concentrated from urine by a simple and fast centrifugation-based urine pretreatment method. Novel automated GenomEra technology was utilized for the rapid closed-tube PCR including time-resolved fluorometric detection of the target using lanthanide chelate labeled probes. We have developed a rapid C. trachomatis assay which provides qualitative results in 1 h with diagnostic sensitivity and specificity of 98.7% and 97.3%, respectively. The novel assay can be performed with minimal laboratory expertise and without sophisticated DNA-extraction devices and has performance comparable to current gold standard assays.     

Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains

Macro domains constitute a protein module family found associated with specific histones and proteins involved in chromatin metabolism. In addition, a small number of animal RNA viruses, such as corona- and toroviruses, alphaviruses, and hepatitis E virus, encode macro domains for which, however, structural and functional information is extremely limited. Here, we characterized the macro domains from hepatitis E virus, Semliki Forest virus, and severe acute respiratory syndrome coronavirus (SARS-CoV). The crystal structure of the SARS-CoV macro domain was determined at 1.8-Angstroms resolution in complex with ADP-ribose. Information derived from structural, mutational, and sequence analyses suggests a close phylogenetic and, most probably, functional relationship between viral and cellular macro domain homologs. The data revealed that viral macro domains have relatively poor ADP-ribose 1"-phosphohydrolase activities (which were previously proposed to be their biologically relevant function) but bind efficiently free and poly(ADP-ribose) polymerase 1-bound poly(ADP-ribose) in vitro. Collectively, these results suggest to further evaluate the role of viral macro domains in host response to viral infection.