Retrotransposon BARE1 translation, localization, and VLP formation in barley

Retrotransposons are major components of most eukaryotic genomes. They resemble retroviruses except that their lifecycle is limited to within the boundaries of the cell. In this thesis work, the goal was to understand the replication of the BARE1 retrotransposon which belongs to the Class I LTR (Long Terminal Repeat) transposable elements (TEs) of the Copia superfamily. The BARE family constitutes about 2.9% of the barley (Hordeum vulgare L.) genome. We systemically searched Expressed Sequence Tag (EST) databases for transcriptionally active TEs, and found that BARE and LTR -retrotransposons in general are shared and widely active in grasses. We raised antibodies to the BARE1 capsid (GAG), integrase (INT), and reverse-transcriptase-RNaseH (RT-RH) proteins and showed that the BARE1 is expressed as one polyprotein of 150 kDa, processed into a shorter 90 kDa form after cleavage of the RT-RH, and further into mature-sized GAG and INT. These proteins were present in barley almost constitutively; only drought-stress had a positive effect on the levels of the GAG protein. Our results show, for the first time, that pools of retrotransposon polyproteins in plant cells are conserved and abundant enough to be detected immunologically in wide selection of species in the Gramineae. We studied the potential sites for BARE replication in barley by immune and in situ localizations. Both root and shoot apical meristems showed the presence of the BARE proteins, supporting the strategy that newly inserted copies must be carried clonally to the cells giving rise to gametes in order to survive in succeeding generations. Moreover, the cells in phloem companion cells showed localization that suggests the BARE may be able to move within the vasculature of the barley. Density gradients were used to study whether the BARE forms VLPs in barley cells. Fractions positive for BARE1 GAG and INT were visualized in transmission electron microscopy using negative staining. This was the first time VLPs were demonstrated in any plant. The VLP assembly requires excess amounts of GAG, whereas the BARE1 encodes its proteins in a single open reading frame. We observed three different pools of RNA transcripts, one for the polyprotein translation, one for encapsidation and reverse transcription, and a third one that is spliced so that it can translate only GAG, thus contributing to a comparatively larger pool of GAG. The transcript dedicated for encapsidation lacks both the cap and poly(A) for translatability, but contains the R regions critical for replication into the complementary DNA that can be inserted back into the host genome. Evidence for these new BARE insertions was found by comparing polymorphism revealed by PCR methods between several grass species. Taken together, we found that the BARE elements are capable to accomplish their lifecycle not only in barley, but in grass species in general, and thus contribute to the growth of their genome sizes.Kasvien perimästä suuri osa koostuu toistuvista DNA jaksoista. Retrotransposonit muodostavat tästä toistuvasta DNA:sta pääosan, kattaen eräillä kasveilla jopa 70% perimästä. Retrotransposonit muistuttavat retroviruksia rakenteeltaan ja elinkierroltaan. Ne muodostavat viruksenkaltaisia partikkeleita (virus-like particle, VLP), joista kuitenkin puuttuu solusta ulospääsyyn tarvittava valkuaisaine. VLP:n tehtävänä on kuljettaa retrotransposonien DNA takaisin tumaan, jossa se liitetään takaisin perimään. Uusi kopio on aina perimän mutaatio jonka laatu riippuu paikasta perimässä. Lisäksi perimän koko kasvaa kopioluvun kasvaessa. Tässä väitöskirjatyössä on tutkittu ohran BARE1 retrotransposonin ilmenemistä kasveilla, kuten ohralla. BARE1 on ensimmäinen ohrasta löydetty retrotransposoni. Se kuuluu BARE retrotransposoni perheeseen joka muodostaa noin 2,9% ohran perimästä. Seuloimme yksi- ja kaksisirkkaisten kasvien ilmentyvien geenien osasekvenssejä (Expressed Seguence Tag) aktiivisten retrotransposonien löytämiseksi. Havaitsimme että poiketen kaksisirkkaisista yksisirkkaisilla heinäkasveilla, kuten viljoilla, on yhteisiä aktiivisia retrotransposoneita, kuten BARE1. Valmistimme vasta-aineita BARE1:n valkuaisaineita vastaan ja havaitsimme, että BARE on aktiivinen tuottaen valkuaisaineita kaikissa tutkimissamme vilja- ja heinäkasveissa. Lisäksi BARE aktiivisuuden havaittiin muuttuvan ohrassa kuivastressin aikana, koska VLP:tä muodostavan valkuaisaineen määrät kasvoivat. Tätä tukee myös toisissa tutkimuksissa havaittu BARE kopioluvun kasvu villiohran perimässä mitä kuivemmalla paikalla kasvi on kasvanut. Tutkimme kykeneekö BARE muodostamaan VLP:tä uuttamalla ohran soluja ja erottamalla uutteesta VLP:t tiheysgradientilla. Fraktioiden, jotka sisälsivät BARE1 komponentteja, havaittiin elektronimikroskopian avulla sisältävän myös VLP:tä. Kasveilta ei tätä ennen ole löydetty VLP:tä. Selvitimme VLP:tä muodostavan valkuaisaineen lähetti-RNA molekyylejä ja havaitsimme että BARE1 tuottaa uudenlaisella tavalla kolmea eri RNA populaatiota, yhtä oman perimänsä säilyttämiseen ja kahta muuta valkuaisaineiden tuottoon. Koska kasvit eivät muodosta erillistä sukusolulinjaa, olisi uusien BARE kopioiden selviydyttävä kloonautumalla sukusoluihin. Tutkimme tätä paikantamalla BARE valkuaisaineita immunologisesti ohran solukoissa ja havaitsimme niiden määrät runsaimmiksi kasvupisteissä, mikä tukee teoriaa. Lisäksi valkuaisaineita löytyi myös siiviläputkien seurasoluista viitaten BARE1:n mahdolliseen liikkumiseen johtosolukossa, mikä olisi ennenkuulumatonta. Merkkejä uusista BARE1 kopioista havaitsimme geenimerkkien välisestä polymorfiasta. Tämä opinnäytetyö antaa uusia näkökulmia ja vahvistaa käsitystä retrotransposonien merkityksestä kasvien perimään ja sen kokoon

Method for constructing an AOD-related atmospheric correction time series for the CLARA-A2 SAL data record

In the Satellite Application Facility on Climate Monitoring (CM SAF) project, financially supported by EUMETSAT, the 34-year long (1982-2015) broadband albedo time series CLARA-A2 SAL (the Surface ALbedo from the CM SAF cLoud, Albedo and RAdiation data record, second version) was produced from Advanced Very High Resolution Radiometer (AVHRR) measurements. CLARA-A2 SAL data record uses a Simplified Method for Atmospheric Correction algorithm SMAC for correcting for atmospheric effects. Aerosol optical depth (AOD) is the main input of the algorithm. Because there were no global AOD time series for the whole needed time period (1982-2015), the AOD-related time series were constructed, and the method for calculating it is described in this report

Sagnac Rotational Phase Shifts in a Mesoscopic Electron Interferometer with Spin-Orbit Interactions

The Sagnac effect is an important phase coherent effect in optical and atom interferometers where rotations of the interferometer with respect to an inertial reference frame result in a shift in the interference pattern proportional to the rotation rate. Here we analyze for the first time the Sagnac effect in a mesoscopic semiconductor electron interferometer. We include in our analysis Rashba spin-orbit interactions in the ring. Our results indicate that spin-orbit interactions increase the rotation induced phase shift. We discuss the potential experimental observability of the Sagnac phase shift in such mesoscopic systems

Changes in healthy and unhealthy working life expectancies among older working-age people in Finland, 2000-2017

Background Raising the statutory retirement age has been a common policy response to population ageing, but health problems may restrict labour force participation in older ages. We examined the development of healthy and unhealthy working life expectancies in Finland from 2000 to 2017 using different measures of health problems. Methods Healthy and unhealthy working life expectancies were calculated for the age range 50-65 years using the Sullivan method. The health measures were limiting long-standing illness, self-rated health, mental health problems and self-assessed work ability. Results Healthy working life expectancy was highest when health was measured by work ability. From 2000 to 2017, working years in full ability between the ages 50-65 increased from 6.2 (95% confidence interval 5.9-6.4) to 8.2 (8.0-8.5). Healthy working life expectancy increased also when measured by the other indicators. Unhealthy working years also increased, except when health problems were measured by limiting long-standing illness. The share of years in work increased both within the healthy and the unhealthy years, the increase being larger or equally large for the latter. Within the healthy and unhealthy years measured by the other three indicators, the share of working years increased irrespective of whether work ability was full or limited, but the increase was larger for limited work ability. Conclusions In Finland, healthy working life expectancy has increased irrespective of how health is measured but also working with health problems has become more prevalent. The estimates for healthy working years are highest when a direct measure of work ability is used.Peer reviewe

Association of short poor work ability measure with increased mortality risk : a prospective multicohort study

Publisher Copyright: © Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.OBJECTIVES: To examine whether a single-item measure of self-rated work ability predicts all-cause mortality in three large population-based samples collected in 1978-1980, 2000 and 2017. SETTING: A representative sample of the population of Finland. PARTICIPANTS: The study population comprised 17 178 participants aged 18 to 65 from the population-based Mini-Finland, Health 2000 and FinHealth 2017 cohort studies, pooled together. In all cohorts, self-rated work ability was assessed at baseline (1978-80, 2000-2001 and 2017) using three response alternatives: completely fit (good work ability), partially disabled (limited work ability) and completely disabled (poor work ability) for work. PRIMARY AND SECONDARY OUTCOME MEASURES: All-cause mortality from national registers. Cox proportional hazards models were adjusted for socioeconomic characteristics, lifestyle factors, self-rated health and mental health problems. RESULTS: Of the participants, 2219 (13%) were classified as having limited and 991 (5.8%) poor work ability and 246 individuals died during the 4 year follow-up. The age- and sex-adjusted HR for mortality risk was 7.20 (95% CI 5.15 to 10.08) for participants with poor vs good work ability and 3.22 (95% CI 2.30 to 4.43) for participants with limited vs good work ability. The excess risk associated with poor work ability was seen in both genders, all age groups, across different educational levels, self-rated health levels and in those with and without mental health problems. The associations were robust to further adjustment for education, health behaviours, self-rated health and mental health problems. In the multivariable analyses, the HR for mortality among those with poor vs good work ability was 5.75 (95% CI 3.59 to 9.20). CONCLUSIONS: One-item poor self-rated work ability -measure is a strong predictor of increased risk of all-cause mortality and may be a useful survey-measure in predicting severe health outcomes in community-based surveys.Peer reviewe

BARE Retrotransposons Are Translated and Replicated via Distinct RNA Pools

Peer reviewe

Precision phenotyping of a barley diversity set reveals distinct drought response strategies

Plants exhibit an array of drought responses and adaptations, where the trade-off between water loss and CO2 uptake for growth is mediated by regulation of stomatal aperture in response to soil water content (SWC), among other factors. For crop yield stability, the question is how drought timing and response patterns relate to post-drought growth resilience and vigor. We earlier identified, in a few reference varieties of barley that differed by the SWC at which transpiration was curtailed, two divergent water use strategies: water-saving (“isohydric”) and water-spending (“anisohydric”). We proposed that an isohydric strategy may reduce risk from spring droughts in climates where the probability of precipitation increases during the growing season, whereas the anisohydric is consistent with environments having terminal droughts, or with those where dry periods are short and not seasonally progressive. Here, we have examined drought response physiology in an 81-line barley (Hordeum vulgare L.) diversity set that spans 20th century European breeding and identified several lines with a third, dynamic strategy. We found a strong positive correlation between vigor and transpiration, the dynamic group being highest for both. However, these lines curtailed daily transpiration at a higher SWC than the isohydric group. While the dynamic lines, particularly cv Hydrogen and Baronesse, were not the most resilient in terms of restoring initial growth rates, their strong initial vigor and high return to initial transpiration rates meant that their growth nevertheless surpassed more resilient lines during recovery from drought. The results will be of use for defining barley physiological ideotypes suited to future climate scenarios

Severe drought in Finland : Modeling effects on water resources and assessing climate change impacts

Severe droughts cause substantial damage to different socio-economic sectors, and even Finland, which has abundant water resources, is not immune to their impacts. To assess the implications of a severe drought in Finland, we carried out a national scale drought impact analysis. Firstly, we simulated water levels and discharges during the severe drought of 1939–1942 (the reference drought) in present-day Finland with a hydrological model. Secondly, we estimated how climate change would alter droughts. Thirdly, we assessed the impact of drought on key water use sectors, with a focus on hydropower and water supply. The results indicate that the long-lasting reference drought caused the discharges to decrease at most by 80% compared to the average annual minimum discharges. The water levels generally fell to the lowest levels in the largest lakes in Central and South-Eastern Finland. Climate change scenarios project on average a small decrease in the lowest water levels during droughts. Severe drought would have a significant impact on water-related sectors, reducing water supply and hydropower production. In this way drought is a risk multiplier for the water–energy–food security nexus. We suggest that the resilience to droughts could be improved with region-specific drought management plans and by including droughts in existing regional preparedness exercises

A non-targeted LC-MS metabolic profiling of pregnancy : longitudinal evidence from healthy and pre-eclamptic pregnancies

IntroductionMaternal metabolism changes substantially during pregnancy. However, few studies have used metabolomics technologies to characterize changes across gestation.Objectives and methodsWe applied liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics to determine whether the metabolic profile of serum differs throughout the pregnancy between pre-eclamptic and healthy women in the FINNPEC (Finnish Genetics of Preeclampsia Consortium) Study. Serum samples were available from early and late pregnancy.ResultsProgression of pregnancy had large-scale effects to the serum metabolite profile. Altogether 50 identified metabolites increased and 49 metabolites decreased when samples of early pregnancy were compared to samples of late pregnancy. The metabolic signatures of pregnancy were largely shared in pre-eclamptic and healthy women, only urea, monoacylglyceride 18:1 and glycerophosphocholine were identified to be increased in the pre-eclamptic women when compared to healthy controls.ConclusionsOur study highlights the need of large-scale longitudinal metabolomic studies in non-complicated pregnancies before more detailed understanding of metabolism in adverse outcomes could be provided. Our findings are one of the first steps for a broader metabolic understanding of the physiological changes caused by pregnancy per se.Peer reviewe