A generalized stoichiometric model of C3, C2, C2+C4, and C4 photosynthetic metabolism.

The goal of suppressing photorespiration in crops to maximize assimilation and yield is stimulating considerable interest among researchers looking to bioengineer carbon-concentrating mechanisms into C3 plants. However, detailed quantification of the biochemical activities in the bundle sheath is lacking. This work presents a general stoichiometric model for C3, C2, C2+C4, and C4 assimilation (SMA) in which energetics, metabolite traffic, and the different decarboxylating enzymes (NAD-dependent malic enzyme, NADP-dependent malic enzyme, or phosphoenolpyruvate carboxykinase) are explicitly included. The SMA can be used to refine experimental data analysis or formulate hypothetical scenarios, and is coded in a freely available Microsoft Excel workbook. The theoretical underpinnings and general model behaviour are analysed with a range of simulations, including (i) an analysis of C3, C2, C2+C4, and C4 in operational conditions; (ii) manipulating photorespiration in a C3 plant; (iii) progressively upregulating a C2 shuttle in C3 photosynthesis; (iv) progressively upregulating a C4 cycle in C2 photosynthesis; and (v) manipulating processes that are hypothesized to respond to transient environmental inputs. Results quantify the functional trade-offs, such as the electron transport needed to meet ATP/NADPH demand, as well as metabolite traffic, inherent to different subtypes. The SMA refines our understanding of the stoichiometry of photosynthesis, which is of paramount importance for basic and applied research

Whole exome sequencing of benign pulmonary metastasizing leiomyoma reveals mutation in the BMP8B gene

Background: Benign metastasizing leiomyoma (BML) is an orphan neoplasm commonly characterized by pulmonary metastases consisting of smooth muscle cells. Patients with BML have usually a current or previous uterine leiomyoma, which is therefore suggested to be the most probable source of this tumour. The purpose of this case report was to determine the possible genetic grounds for pulmonary BML. Case presentation: We present a case report in an asymptomatic 44-year-old female patient, who has developed uterine leiomyoma with subsequent pulmonary BML. Whole exome sequencing (WES) was used to detect somatic mutations in BML lesion. Somatic single nucleotide mutations were identified by comparing the WES data between the pulmonary metastasis and blood sample of the same BML patient. One heterozygous somatic mutation was selected for validation by Sanger sequencing. Clonality of the pulmonary metastasis and uterine leiomyoma was assessed by X-chromosome inactivation assay. Conclusions: We describe a potentially deleterious somatic heterozygous mutation in bone morphogenetic protein 8B (BMP8B) gene (c.1139A > G, Tyr380Cys) that was identified in the pulmonary metastasis and was absent from blood and uterine leiomyoma, and may play a facilitating role in the metastasizing of BML. The clonality assay confirmed a skewed pattern of X-chromosome inactivation, suggesting monoclonal origin of the pulmonary metastases.Peer reviewe

The rate of nitrite reduction in leaves as indicated by O2 and CO2 exchange during photosynthesis

Light response (at 300 ppm CO2 and 10–50 ppm O2 in N2) and CO2 response curves [at absorbed photon fluence rate (PAD) of 550 μmol m−2 s−1] of O2 evolution and CO2 uptake were measured in tobacco (Nicotiana tabacum L.) leaves grown on either NO3− or NH4+ as N source and in potato (Solanum tuberosum L.), sorghum (Sorghum bicolor L. Moench), and amaranth (Amaranthus cruentus L.) leaves grown on NH4NO3. Photosynthetic O2 evolution in excess of CO2 uptake was measured with a stabilized zirconia O2 electrode and an infrared CO2 analyser, respectively, and the difference assumed to represent the rate of electron flow to acceptors alternative to CO2, mainly NO2−, SO42−, and oxaloacetate. In NO3−-grown tobacco, as well as in sorghum, amaranth, and young potato, the photosynthetic O2–CO2 flux difference rapidly increased to about 1 μmol m−2 s−1 at very low PADs and the process was saturated at 50 μmol quanta m−2 s−1. At higher PADs the O2–CO2 flux difference continued to increase proportionally with the photosynthetic rate to a maximum of about 2 μmol m−2 s−1. In NH4+-grown tobacco, as well as in potato during tuber filling, the low-PAD component of surplus O2 evolution was virtually absent. The low-PAD phase was ascribed to photoreduction of NO2− which successfully competes with CO2 reduction and saturates at a rate of about 1 μmol O2 m−2 s−1 (9% of the maximum O2 evolution rate). The high-PAD component of about 1 μmol O2 m−2 s−1, superimposed on NO2− reduction, may represent oxaloacetate reduction. The roles of NO2−, oxaloacetate, and O2 reduction in the regulation of ATP/NADPH balance are discussed

Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice

The higher photosynthetic potential of C4 plants has led to extensive research over the past 50 years, including C4-dominated natural biomes, crops such as maize, or for evaluating the transfer of C4 traits into C3 lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non-specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C4 photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C4 data analysis accessible to a broader audience. Outputs include those defining C4 photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO2 diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C4 organism and key global crop) to illustrate the approaches, their analysis and interpretation

2022. aasta inimgeneetikas

Eesti Arst 2023; 102(1):46–4

Recycled returned concrete

Ehitusinseneriõppe lõputöö Maaehituse õppekavalKäesolevas magistritöös uuriti tagastatud vedela betooni taaskasutamist uue betoonisegu koostamisel. Töö annab ülevaate taaskasutamisest nii Eestis kui ka mujal maailmas. Üha rohkem on üle maailma hakatud pooldama ja tegelema taaskasutamisega, kuna toorainetena kasutatavaid loodusvarasid ei jätku lõpmatuseni. Betoon on maailmas ka enim kasutatav ehitusmaterjal ja enimkasutatud ressurss vee järel. Tagastatud betoon on segu, mis tuuakse betooniveokitega tehasesse tagasi ja nimetatakse üleliigseks materjaliks. Töö eesmärk on uurida betoonisegusid, mis sisaldavad tagastatud betooni. Magistritöös uuriti erinevaid betoonisegusid, mis sisaldasid 0%, 20%, 40% ja 60% taaskasutatavat seisvat betooni. Uuriti betoonisegude omadusi, nagu survetugevus, töödeldavus, lisatud vee mõju, õhusisaldust ning tsemendi tardumisaega. Kivistunud betooni puhul võrreldi survetugevust valmis segatud ja aeglaselt tarduvas betoonis, mis on segatud uuesti ringlusse võetud betooniga. Katseteks kasutati kahte erineva tugevusklassiga betooni ning selgus, et teatud kogus betoonisegust on võimalik asendada taaskasutatava betooniga. Paremad tulemused saadi betooni tugevusklassiga C35/45, kus vajaliku tugevuse saavutasid kõik katsekehad. Tund aega seisnud taaskasutatav betoon (segus 60%) oli segatud värske betooniga (segus 40%) ning peale 28 päeva saadi keskmiseks survetugevuseks 48,71 MPa. Kaks tundi seisnud taaskasutatav betoon (segus 40%) segati värske betooniga (segus 60%) ning keskmiseks survetugevuseks saadi 49,08 MPa. Kolm tundi seisnud taaskasutatav betoon (segus 20%) segati värske betooniga (segus 80%) ning keskmiseks survetugevuseks saadi 50,79 MPa. Tugevama tugevusega (C50/60) betoonil tuleb kasutada väiksem kogus taaskasutatavat betoonisegu. Tund aega seisnud taaskasutatav betoon (segus 60%) oli segatud värske betooniga (segus 40%) ning peale 28 päeva saadi keskmiseks survetugevuseks 57,76 MPa. Kaks tundi seisnud taaskasutatav betoon (segus 40%) segati värske betooniga (segus 60%) ning keskmiseks survetugevuseks saadi 55,14 MPa. Kolm tundi seisnud taaskasutatav betoon (segus 20%) segati värske betooniga (segus 80%) ning keskmiseks survetugevuseks saadi 61,47 MPa. Katsete põhjal saab järeldada, et kolm tundi seisnud betooni on võimalik kasutada kogu tema olekus uuesti värske betooni koostamisel. Asendades 20% värsket betooni taaskasutatava betooniga saab vajaliku survetugevuse kätte. Edaspidi tuleks täiendavalt uurida, milline on taaskasutatava betoonisegu külmakindlus.In this master's thesis, the reuse of returned liquid concrete in the making of a new concrete mix was investigated. The work provides an overview of reuse both in Estonia and elsewhere in the world. There is growing support around the world and deal with recovery because resources do not last indefinitely. Concrete is also the most used building material and resource after water in the world. Returned concrete is a mixture that is brought back to the factory by concrete trucks and is called surplus material. The aim of the work is to study concrete mixtures that contain returned concrete. In the master's thesis, different concrete mixtures were studied, which contained 0%, 20%, 40% and 60% recyclable standing concrete. In the case of hardened concrete, the compressive strength was compared in ready-mixed and slow-setting concrete mixed with recycled concrete. The concrete mixtures were studied with Abrams cone, added water, air content in the concrete, compressive strength and setting time of the cement. Two different strength classes of concrete were used for the experiments and it was found that a certain amount of concrete mix can be replaced by recycled concrete. Better results were obtained with a lower strength class (C35/45), where the required strength was achieved by all test specimens. The recyclable concrete (in the mixture 60%) that had been standing for one hour, was mixed with fresh concrete (in the mixture 40%) and after 28 days the average compressive strength was 48,71 MPa. After two hours the recycled concrete (in the mixture 40%) was mixed with fresh concrete (in the mixture 60%) and the average compressive strength was 49,08 MPa. After three hours the recycled concrete (in the mixture 20%) was mixed with fresh concrete (in the mixture 80%) and the average compressive strength was 50,79 MPa. For stronger strength (C50/60) concrete, a smaller amount of reusable concrete mix must be used. The recycled concrete (60% in the mix) that had been standing for one hour was mixed with fresh concrete (40% in the mix) and after 28 days the average compressive strength was 57.76 MPa. After two hours, the recycled concrete (in the mixture 40%) was mixed with fresh concrete (in the mixture 60%) and the average compressive strength was 55,14 MPa. After three hours the recycled concrete (in the mixture 20%) was mixed with fresh concrete (in the mixture 80%) and the average compressive strength was 61,47 MPa. From the tests, it can be concluded that the concrete, which has been standing for three hours, can be used in its entire state in the preparation of fresh concrete. By replacing 20% of fresh concrete with recycled concrete, the required compressive strength is obtained. The frost resistance of the recycled concrete mix should be further investigated in the future

Geneetiline varieeruvus kui naisepoolse viljatuse eelsoodumuse mõjutaja ja võimalike uute biomarkerite allikas

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Üks tark mees on öelnud, et lapse saamine on üks ebatõenäoline protsess, ja arvestades seda, kui paljud paarid on viljatusega hädas, oli tal ilmselt õigus. Eestis on enamik naisepoolse viljatuse juhtudest tingitud peamiselt infektsioonide põhjustatud munajuhaviljatusest ja polütsüstiliste munasarjade sündroomist (PCOS), millele on iseloomulik meessuguhormoonide kõrgenenud tase ja insuliinresistentsus. Kunstlik viljastamine võib aidata sellistel juhtudel järglasi saada, kuid kahjuks on ravi tulemuslikkus ~30% ja sõltub suuresti sellest, kuidas munasarjad reageerivad ravi käigus kasutatavatele hormoonidele. Viljatuse molekulaarseid tagamaid on aastate jooksul palju uuritud ja on jõutud järeldusele, et individuaalne geneetiline varieeruvus mängib selle tekkes kindlasti olulist rolli. Geneetilise varieeruvuse uuringud võimaldavad leida ka biomarkereid, mis sobiksid reproduktiivpotentsiaali ja ehk isegi viljatusravi tulemuslikkuse ennustamiseks. Käesoleva töö üldine eesmärk oli hinnata seoseid erinevate geneetiliste variatsioonide ja PCOS-i ning munajuhaviljatuse vahel. Lisaks uurisime mitmeid menopausi algusajaga või munasarja funktsiooniga seotud geneetilisi variante, mis võiksid olla seotud reproduktiivpotentsiaali ja viljatusravi tulemuslikkuse parameetritega. Selle jaoks koguti tervete ja viljakusprobleemidega naiste DNA proovid ning analüüsiti 47 geneetilise variandi seost huvipakkuvate diagnooside ja kliiniliste tunnustega. Et teha kindlaks, kui suur osa munajuhaviljatuse juhtudest on tingitud urogenitaalsest klamüüdiainfektsioonist, määrati munajuhaviljatusega naiste vereseerumist klamüüdia-vastaste antikehade esinemine. Leidsime, et ~50% kõigist munajuhaviljatuse juhtudest võivad olla tingitud eelnevast klamüüdiainfektsioonist ja näitasime, et immuunvastust mõjutav mannoosi siduva lektiini geeni varieeruvus on ilmselt seotud munajuhaviljatuse geneetilise eelsoodumusega. Insuliini ja androgeeni retseptori geenide varieeruvus ei olnud seotud PCOS-iga. Lisaks näitasime, et menopausi algusaega mõjutavad geenivariandid on seotud munasarja funktsiooni ja viljatusravi tulemuslikkuse parameetritega, ja tulevikus võiks neid kombineerituna kliiniliste andmetega kaaluda võimalike biomarkeritena. Antud töö andis uut teavet naise viljakuse ja viljatuse geneetika kohta, kuid ühtlasi rõhutas edasiste uuringute vajalikkust.A wise man once said that the reproduction of mankind is a great marvel and mystery, and he was absolutely right, considering how many couples actually tackle with infertility. In Estonia, the majority of female infertility cases are due to tubal infertility (TFI) that is mostly caused by sexually transmitted infections, and polycystic ovary syndrome (PCOS), which is an endocrine disorder characterised by androgen excess and insulin resistance. In vitro fertilisation can help achieve pregnancy in these cases, but unfortunately the pregnancy rate per treatment cycle is only 30% and depends greatly on how the ovaries respond to the treatment. Over the years, great effort has been directed towards elucidating the molecular mechanisms behind the conditions causing infertility and it has been concluded that individual genetic variation is definitely one of the factors to blame. The studies of individual genetic variation form a good basis for finding biomarkers to predict natural reproductive function and perhaps even infertility treatment success. The general objective of the current thesis was to assess the associations between PCOS, TFI and selected candidate genes. In addition, several genetic variants that could be related to ovarian function and infertility treatment parameters were evaluated. Thus, DNA samples were collected from healthy women and infertile women and 47 genetic variants were studied in association with diagnoses of interest and different clinical parameters. In addition, to determine how many TFI cases are caused by a chlamydia infection, the prevalence of chlamydia-specific antibodies was measured in the blood sera of women with TFI. As a result, we found that ~50% of all TFI cases in Estonia might be caused by a previous chlamydia infection and identified genetic variants in the mannose binding lectin gene that modulate immune response and may be associated with susceptibility to TFI. No associations were found between selected variants in genes for insulin and androgen receptor and PCOS. However, we showed that genetic variants related to menopause timing are associated with ovarian function and infertility treatment parameters and could be considered as biomarker candidates if combined with clinical data. In conclusion, this study gave new knowledge about the genetics of female reproduction, but also highlighted the need for further research

Enhancing cross-institute generalisation of GNNs in histopathology through multiple embedding graph augmentation (MEGA)

Many recent methods for the analysis of histology whole slide images (WSIs) have used graph neural networks (GNNs) to aggregate visual information over a large image resolution. However, domain shift is a significant challenge in computational histopathology, due to differences in WSI appearance between institutes, and the effect of these differences on training GNNs has not been explored. In this work, we present the Multiple Embedding Graph Augmentation (MEGA) strategy to improve the cross-institute generalisation of GNNs in histology. We show that by introducing image augmentation and normalisation to the node features used to train a GNN, we can train a model that is robust to domain shift without additional labels or further training of the feature extractor. We compare MEGA to noise-based regularisation and demonstrate its effectiveness in a node classification tissue prediction task in placenta histology

Genome-wide association study meta-analysis supports association between MUC1 and ectopic pregnancy

Abstract Study question: Can we identify genetic variants associated with ectopic pregnancy by undertaking the first genome-wide association study (GWAS) leveraging two large-scale biobank initiatives? Summary answer: We identified two novel genome-wide significant associations with ectopic pregnancy, highlighting MUC1 (mucin 1) as the most plausible affected gene. What is known already: Ectopic pregnancy is an important cause of maternal morbidity and mortality worldwide. Despite being a common early pregnancy complication, the genetic predisposition to this condition remains understudied and no large scale genetic studies have been performed so far. Study design, size, duration: A GWAS meta-analysis including 7070 women with ectopic pregnancy and 248 810 controls from Estonian Biobank and the FinnGen study. Participants/materials, setting, methods: We identified ectopic pregnancy cases from national registers by ICD (International Classification of Disease) codes (ICD-10 O00), and all remaining women were considered controls. We carried out standard GWAS meta-analysis and additionally annotated GWAS signals, analysed co-localization with quantitative trait loci, estimated genetic correlations and identified associated phenotypes to characterize the genetic signals, as well as to analyse the genetic and phenotypic relationships with the condition. Main results and the role of change: We identified two genome-wide significant loci on chromosomes 1 (rs4971091, P = 5.32x10−9) and 10 (rs11598956, P = 2.41x10−8) potentially associated with ectopic pregnancy. Follow-up analyses propose MUC1, which codes for an epithelial glycoprotein with an important role in barrier function, as the most likely candidate gene for the association on chromosome 1. We also characterize the phenotypic and genetic correlations with other phenotypes, identifying a genetic correlation with smoking and diseases of the (genito)urinary and gastrointestinal system, and phenotypic correlations with various reproductive health diagnoses, reflecting the previously known epidemiological associations. Large scale data: The GWAS meta-analysis summary statistics are available from the GWAS Catalogue (GCST90272883). Limitations, reasons for caution: The main limitation is that the findings are based on European-based ancestry populations, with limited data on other populations, and we only captured maternal genomes. Additionally, further larger meta-analysis or independent studies are needed to validate these findings. Wider implications of the findings: This study encourages the use of large-scale genetic datasets to unravel genetic factors linked to ectopic pregnancy, which is difficult to study in experimental settings. Increased sample size might bring additional genetic factors associating with ectopic pregnancy and inform its heritability. Altogether, our results provide more insight into the biology of ectopic pregnancy and, accordingly, the biological processes governing embryo implantation. Study funding(competing interest(s): N.P.G. was supported by MATER Marie Sklodowska-Curie which received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 813707. This study was funded by European Union through the European Regional Development Fund Project No. 2014-2020.4.01.15-0012 GENTRANSMED. Computations were performed in the High-Performance Computing Center of University of Tartu. The authors declare no competing interests.Abstract Study question: Can we identify genetic variants associated with ectopic pregnancy by undertaking the first genome-wide association study (GWAS) leveraging two large-scale biobank initiatives? Summary answer: We identified two novel genome-wide significant associations with ectopic pregnancy, highlighting MUC1 (mucin 1) as the most plausible affected gene. What is known already: Ectopic pregnancy is an important cause of maternal morbidity and mortality worldwide. Despite being a common early pregnancy complication, the genetic predisposition to this condition remains understudied and no large scale genetic studies have been performed so far. Study design, size, duration: A GWAS meta-analysis including 7070 women with ectopic pregnancy and 248 810 controls from Estonian Biobank and the FinnGen study. Participants/materials, setting, methods: We identified ectopic pregnancy cases from national registers by ICD (International Classification of Disease) codes (ICD-10 O00), and all remaining women were considered controls. We carried out standard GWAS meta-analysis and additionally annotated GWAS signals, analysed co-localization with quantitative trait loci, estimated genetic correlations and identified associated phenotypes to characterize the genetic signals, as well as to analyse the genetic and phenotypic relationships with the condition. Main results and the role of change: We identified two genome-wide significant loci on chromosomes 1 (rs4971091, P = 5.32x10−9) and 10 (rs11598956, P = 2.41x10−8) potentially associated with ectopic pregnancy. Follow-up analyses propose MUC1, which codes for an epithelial glycoprotein with an important role in barrier function, as the most likely candidate gene for the association on chromosome 1. We also characterize the phenotypic and genetic correlations with other phenotypes, identifying a genetic correlation with smoking and diseases of the (genito)urinary and gastrointestinal system, and phenotypic correlations with various reproductive health diagnoses, reflecting the previously known epidemiological associations. Large scale data: The GWAS meta-analysis summary statistics are available from the GWAS Catalogue (GCST90272883). Limitations, reasons for caution: The main limitation is that the findings are based on European-based ancestry populations, with limited data on other populations, and we only captured maternal genomes. Additionally, further larger meta-analysis or independent studies are needed to validate these findings. Wider implications of the findings: This study encourages the use of large-scale genetic datasets to unravel genetic factors linked to ectopic pregnancy, which is difficult to study in experimental settings. Increased sample size might bring additional genetic factors associating with ectopic pregnancy and inform its heritability. Altogether, our results provide more insight into the biology of ectopic pregnancy and, accordingly, the biological processes governing embryo implantation. Study funding(competing interest(s): N.P.G. was supported by MATER Marie Sklodowska-Curie which received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 813707. This study was funded by European Union through the European Regional Development Fund Project No. 2014-2020.4.01.15-0012 GENTRANSMED. Computations were performed in the High-Performance Computing Center of University of Tartu. The authors declare no competing interests