Moving Beyond Co-Construction of Knowledge to Enable Self‑Determination

It is increasingly recognised that co-construction of knowledge which brings together researcher-derived understanding, with local, practitioner or non-researcher understanding is necessary to address current global challenges. Emerging empirical evidence suggests challenges remain in bridging across scales and ensuring inclusion of the marginalised. It is unclear whether espoused approaches are in practice enhancing the wellbeing of those currently on the front lines of ecological, social and political crises, or, whether they are inadvertently increasing inequality. In this article, we explore co-construction from our experience as embedded researcher–practitioners through two case studies: the ecological restoration of fisheries by the Skolt Sámi in Finland, and the conservation of agro-ecological and forest management practices by peasant communities in Paraguay. We challenge the idea that co-construction of knowledge is sufficient to engage with regressive institutional and political dynamics that continue to marginalise, arguing for a focus on self-determination to be the foundation for co-construction

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

Background: Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. Results: In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. Conclusions: In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Genetic diversity of a clonal earthworm : gene expression variation and impacts on decomposition in metal contaminated soil

Biodiversity affects ecosystem functioning positively. Metal-contamination diminishes species diversity and ecosystem function depends on the remaining species, and the genotypes within them. I studied how the clonally reproducing earthworm Dendrobaena octaedra responds to soil metal contamination and how its genetic diversity affects decomposition. Expression of the gene for the metal tolerance protein metallothionein was compared between populations with or without metal exposure history: with exposure history expression was high and stable and without there was a slow response. Adaptation to metal contamination likely explains the differences. Clonality of D. octaedra was verified with microsatellite markers. However, there was considerable gene expression variation both between and within genotypes, highlighting the need to consider such variation in comparative gene expression studies. The main study question focused on if genetic diversity is important for ecosystem functioning in metalcontaminated soil. I manipulated genetic diversity of a key decomposer, D. octaedra in a microcosm experiment. Indications of positive effects of higher genetic diversity on decomposition were found, especially in the contaminated conditions. However, the differences between the treatments often depended on which genotype was in the low diversity treatment, suggesting that traits of the genotypes might be more important than the level of genetic diversity for ecosystem functioning. An alternative technique to the real-time quantitative PCR, droplet digital PCR, was tested for gene expression measurements, and found to be a promising technique

Software tools in medical genetics : a systematic mapping study

Kaupallisten geenitestien tarjonnan kasvu ja kokonaisten genomien sekvensoinnin muuttuminen yhä helpommaksi ja halvemmaksi mahdollistavat geneettisen tiedon hyödyntämisen lääketieteessä. Tästä on paljon hyötyä terveydenhoidossa, mutta siihen liittyy myös haasteita. Haasteita tuovat mm. geeniteknologian tuottamien suurten datamäärien varastointi, jakaminen ja käsittely, geneettisen datan analysointi niin, että oleellinen tieto saadaan selville ja monimutkaisen geneettisen datan tulkitseminen ja visualisointi ymmärrettävässä muodossa. Geneettisen datan suojaaminen on myös yksi suuri haaste lääketieteellisessä genetiikassa. Tehokkaat ja hyvin suunnitellut digitaaliset työkalut voivat auttaa näissä haasteissa, ja uusille työkaluille onkin kasvava tarve, kun lääketieteellinen genetiikka yleistyy. Tässä tutkimuksessa pyrin tekemään systemaattisen kartoituksen lääketieteellisen genetiikan digitaalisista työkaluista ja vastaamaan kysymyksiin siitä, millaisia tutkimuksia aiheesta on, millainen teknologinen fokus niissä on, onko datan suojaamista käsitelty artikkeleissa ja minkä tyyppisissä tieteellisissä lehdissä artikkeleita on julkaistu. Tuloksista selviää, että suurin osa artikkeleista on validointitutkimuksia. Tämä tulos johtuu luultavasti osittain siitä, miten kriteerit artikkelin mukaan ottamiseen on määritetty ja miten kategorisointi on tehty. Suurin osa artikkeleista käsittelee geneettisen datan esikäsittelyä ja analysointia, mikä johtuu luultavasti siitä, että geneettistä dataa on niin monenlaista ja sen analysointi on vaikeaa, jolloin on tarvetta monille erilaisille digitaalisille työkaluille auttamaan siinä. Datan suojaamista ei käsitellä suurimmassa osassa artikkeleita, mutta se johtunee ainakin osittain siitä, että datan suojaamisen ei katsota olevan oleellista kaiken tyyppisissä digitaalisissa työkaluissa. Suurin osa artikkeleista oli julkaistu lehdissä, jotka liittyvät lääketieteelliseen genetiikkaan (genetiikka, lääketiede ja bioinformatiikka) ja julkaisuja ei ollut juurikaan yleisemmin tietotekniikkaa käsittelevissä lehdissä. Tämä johtunee siitä että, lääketieteellisen genetiikan digitaalisia työkaluja käyttävät luultavasti lähinnä alan ammattilaiset, jotka lukevat enemmän genetiikkaan liittyviä julkaisuja kuin yleisesti ohjelmistoihin keskittyviä lehtiä.Rise of commercial gene tests and whole-genome sequencing becoming easier and cheaper brings many benefits to health care, but also challenges. The challenges include storing, sharing and managing huge amounts of data, analyzing genetic data to find rele-vant information, and interpreting and visualizing complex genetic data. The issue of data privacy is also a major concern in medical genetics. Efficient and well-designed software can help with these challenges. In my thesis, I strive to provide a systematic mapping of the literature on medical genetics software and answer questions about what types of re-search approaches and technological focuses there are in scientific articles on the subject, is data privacy addressed in the articles, and what types of journals the articles are published in. The results show that validation is the most common research approach. This result is possibly partly due to the inclusion criteria and categorization approach used. Preprocessing and analysis of genetic data is the most common technological focus in the papers, likely due to genetic data and analysis of it being very complex and requiring dif-ferent kinds of software to help with it. Data privacy is not addressed in most of the papers, which could partly be due to it not deemed an issue in all types of software. Most of the articles were published in journals related to medical genetics, which is probably due to the genetics professionals using the software reading more journals related to their field

Variation in gene expression within clones of the earthworm Dendrobaena octaedra

Abstract Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones) is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor) also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes

Pygospio_genotype_data

The 'Pygospio_genotype_data.txt' file contains microsatellite genotype data of 765 P. elegans individuals used in the study. There is 2 to 3 temporal samples collected from 7 different European collection sites

Gene expression (RQ) in offspring of each family.

<p>The box plot shows all the individuals of the family (median, 25% upper and lower quartile, minimum, maximum, and outliers).</p