Biology subjects

Bucholc, M.

Publications and source records attributed to Bucholc, M..

7 recordsLinked to original sources

bioRxiv2025

SnRK2.4 and SnRK2.10 redundantly control developmental leaf senescence by sustaining ABA production and signaling

Plants constantly and precisely control their growth by inducing distinct developmental programs to survive and produce high-quality offspring in the changing environment. The fine-tuning of the development according to endogenous and environmental signals requires exact intercellular signaling and a balanced response. Kinases of the Sucrose non-fermenting-1-Related protein Kinases type 2 (SnRK2s) family primarily take part in the response and adaptation to environmental stress factors. Notably, here we show that two ABA-non-activated SnRK2s, SnRK2.4 and SnRK2.10, are also activated in non-stress conditions in developmentally senescing leaves of Arabidopsis thaliana. Phenotypic, biochemical, and molecular analyses performed on single snrk2.4 or snrk2.10, and double snrk2.4/2.10 kinase mutants showed that SnRK2.4 and SnRK2.10, acting redundantly, promote developmental leaf senescence. Further, SnRK2.4 and SnRK2.10 enhance ABA accumulation in senescing leaves by inducing NCED2, one of key ABA biosynthesis-related genes. The two kinases induce developmental leaf senescence by modulating the expression of multiple ABA-responsive, osmotic stress, and senescence-related genes, such as the senescence master regulators ORE1, ORS1, WRKY33, WRKY75, and ANAC087. Furthermore, we show that SnRK2.4 and SnRK2.10 act upstream of MAPK signaling by enhancing the expression and activity of MAPKKK18, a senescence-inducing kinase. These results document a new regulatory function of SnRK2.4 and SnRK2.10: they are activated in Arabidopsis leaves in response to endogenous signals and redundantly induce developmental leaf senescence by stimulating ABA production and sustaining major ABA-dependent and -independent signaling pathways.

plant biology↗

bioRxiv2023

Phosphorylation Promotes Liquid-Liquid Phase Separation of GRP8 and Its Assembly into Stress Granules Upon Salinity Stress in Arabidopsis

Drought and salinity are major environmental stresses affecting plant development and growth. SNF1-related protein kinases type 2 (SnRK2s) are key regulators of the plant responses to water deficit and salt stress. Here, we show that Arabidopsis thaliana Glycine-Rich RNA-Binding Protein 8 (GRP8) is a target of abscisic acid (ABA)-non-activated SnRK2s and negatively regulates root growth and seed germination under salt stress. In response to salinity, GRP8 assembles into stress granules (SGs). We show that in addition to the GRP8 C-terminal glycine-rich intrinsically disordered region (IRD), the N-terminal RNA recognition motif (RRM) plays a key role in this process. Phosphorylation of S27 in the RRM by SnRK2s significantly affects the structural dynamics of GRP8, facilitates its dimerization and subsequent liquid-liquid phase separation. Thus, we show that in addition to the known role of IDRs in recruitment into SGs, the RRM plays a decisive role.

plant biology↗

bioRxiv2019

Biochemical, Biophysical, and Functional Analyses of Two Isoforms of the SnRK2 Inhibitor AtSCS

SNF1-related protein kinases 2 (SnRK2s) are key signaling elements that regulate abscisic acid (ABA)-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) is an inhibitor of SnRK2 activity. In Arabidopsis thaliana, the use of alternative transcription start sites located within AtSCS gene results in two in-frame transcripts and subsequently two proteins, which differ only by the sequence position of the N-terminus. We described the longer AtSCS-A earlier, and now we describe the shorter AtSCS-B and compare both isoforms. The two forms differ significantly in their expression profiles in plant organs and in response to environmental stresses, in calcium binding properties, and conformational dynamics in the presence and absence of Ca2+. The results show that only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but differ with respect to calcium dependence, as AtSCS-A requires calcium for inhibition, while AtSCS-B does not. Analysis of Arabidopsis plants stably expressing 35S::AtSCS-A-c-myc or 35S::AtSCS-B-c-myc in the scs-1 knockout mutant revealed that in planta both forms are negative regulators of the SnRK2 activity induced in response to ABA and regulate plant defense against water deficit. Moreover, the data present biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.\n\nOne sentence SummaryTwo isoforms of SnRK2-interacting calcium sensor are expressed in Arabidopsis; they differ in calcium binding properties, but both of them inhibit SnRK2s and subsequently fine tune ABA signaling.

plant biology↗

bioRxiv2019

A practical computerized decision support system for predicting the severity of Alzheimer’s disease of an individual

Computerized clinical decision support systems can help to provide objective, standardized, and timely dementia diagnosis. However, current computerized systems are mainly based on the group analysis, discrete classification of disease stages, or expensive and not readily accessible biomarkers, while current clinical practice relies relatively heavily on cognitive and functional assessments (CFA). In this study, we developed a computational framework using a suite of machine learning tools for identifying key markers in predicting the severity of Alzheimers disease (AD) from a large set of biological and clinical measures. Six machine learning approaches, namely Kernel Ridge Regression (KRR), Support Vector Regression (SVR), and k-Nearest Neighbor (kNNreg) for regression and Support Vector Machine (SVM), Random Forest (RF), and k-Nearest Neighbor (kNNclass) for classification, were used for the development of predictive models. We demonstrated high predictive power of CFA. Predictive performance of models incorporating CFA was shown to be consistently higher accuracy than those based solely on biomarker modalities. We found that KRR and SVM were the best performing regression and classification methods respectively. The optimal SVM performance was observed for a set of four CFA test scores (FAQ, ADAS13, MoCA, MMSE) with multi-class classification accuracy of 83.0%, 95%CI = (72.1%, 93.8%) while the best performance of the KRR model was reported with combined CFA and MRI neuroimaging data, i.e., R2 = 0.874, 95%CI = (0.827, 0.922). Given the high predictive power of CFA and their widespread use in clinical practice, we then designed a data-driven and self-adaptive computerized clinical decision support system (CDSS) prototype for evaluating the severity of AD of an individual on a continuous spectrum. The system implemented an automated computational approach for data pre-processing, modelling, and validation and used exclusively the scores of selected cognitive measures as data entries. Taken together, we have developed an objective and practical CDSS to aid AD diagnosis.

neuroscience↗

bioRxiv2019

Primary care use of laboratory tests in Northern Ireland Western Health and Social Care Trust: a cross-sectional study

ObjectivesTo describe the laboratory test ordering patterns by general practitioners (GPs) in Northern Ireland Western Health and Social Care Trust (WHSCT) and establish demographic and socio-economic associations with test requesting.\n\nDesignCross-sectional study.\n\nSettingWestern Health and Social Care Trust, Northern Ireland\n\nParticipants55 WHSCT general practices requesting laboratory tests in the period from 1 April 2011 to 31 March 2016\n\nOutcomesTo identify the temporal patterns of laboratory test ordering behaviour for 8 commonly requested clinical biochemistry tests/test groups in WHSCT. To analyse the extent of variations in laboratory test requests by GPs and to determine whether these variations can be accounted for by clinical outcomes or geographical, demographic, and socioeconomic characteristics.\n\nResultsWe identified substantial changes in the median number of request rates over five consecutive years of the study period as well as a large variation of adjusted test request rates for individual tests (lowest for electrolyte profiles, liver profiles, and HbA1c and highest for immunoglobulins). No statistically significant relationship between ordering activity and either demographic (age and gender) and socioeconomic factors (deprivation) or Quality and Outcome Framework (QOF) scores was observed. We found that practice setting accounted for some of the between-practice variation in test requesting. Rural practices were characterized by both higher between practice variability and median number of order tests than urban practices at all time points.\n\nConclusionsA large between-practice variation in GP laboratory test requesting appears unrelated to demographic and socioeconomic indicators of the practices or crude clinical outcome indicators, most likely reflects differences in the clinical practice of individuals, potentially amenable to change through clinical interventions.\n\nStrengths and limitations of this studyO_LIThe study provides a comprehensive analysis of temporal changes in laboratory test utilization patterns and establishes the extent of variability in test requesting activity across general practices in Northern Irelands Western Health and Social Care Trust.\nC_LIO_LIThe substantial variation in test ordering, not related to demographic and socioeconomic characteristics of practices, practice location or clinical outcome indicators, may reflect inappropriate laboratory test utilization and hence, suggest a potential for more efficient demand management of laboratory services.\nC_LIO_LIGiven a cohort of general practices within one catchment area, our results provide evidence of differences in behaviour of individual GPs when managing patients with similar clinical symptoms.\nC_LIO_LIFailure to collect and cross-tabulate data on characteristics of general practitioners (GPs), such as GPs age, years of experience, medical training was a study limitation and a missed opportunity in assessing the influence of practitioner factors on the variation in test ordering behaviour.\nC_LI

biochemistry↗

bioRxiv2019

Effects of a demand optimization intervention on laboratory test utilization in primary care

There is evidence of increasing use of laboratory tests with substantial variation between clinical teams which is difficult to justify on clinical grounds. The aim of this project was to assess the effect of a demand optimisation intervention project on laboratory test requesting by general practitioners (GPs) in an area of Northern Ireland supported by the Clinical Chemistry Laboratory service of Western Health and Social Care Trust (WHSCT). The intervention package was developed in conjunction with the Western Local Commissioning Group and consisted of educational initiatives, feedback to 55 individual practices on test request rates with ranking relative to other practices, and a small financial incentive for practices to reflect on their test requesting activity. Overall test utilization rates of profile tests, HbA1c, and PSA one year before, during, and one year after the intervention were measured using laboratory databases of the Altnagelvin Area Hospital, Tyrone County Hospital, and the Erne (South West Acute Hospital. The intervention was associated with mixed effects. First, we observed a reduction of 5.1% in the median profile test request rates and a decrease in their between practice variability. The overall downward trend in variability of profile test request rates was found statistically significant (p = 0.03). Second, we found a significant increase in both the volume (p < 0.0001) and between practice variability (p = 0.0001) of HbA1c requests per patient with diabetes. The increase in HbA1c requests may reflect a more appropriate rate of diabetes monitoring and also the adoption of HbA1c as a diagnostic test. Yet, the subsequent 600% increase in between practice variability of HbA1c ordering rates may imply an inconsistent implementation of recommended guidelines by GPs. Finally, there was a 29.3% increase in the median and 35% increase in between practice variability of request rates for PSA, the reasons for which are unclear.

pathology↗

bioRxiv2018

A laboratory demand optimisation project in primary care

BackgroundThere is evidence of increasing use of laboratory tests with substantial variation between clinical teams which is difficult to justify on clinical grounds. The aim of this project was to assess the effect of a demand optimisation intervention on laboratory test requesting in primary care.\n\nMethodsThe intervention comprised educational initiatives, feedback to 55 individual practices on test request rates with ranking relative to other practices, and a small financial incentive for practices to engage and reflect on their test requesting activity. Data on test request numbers were collected from the laboratory databases for consecutive 12 month periods; pre-intervention 2011-12, intervention 2012-13, 2013-14, 2014-15, and post-intervention 2015-16.\n\nResultsThe intervention was associated with a 3.6% reduction in the mean number of profile test requests between baseline and 2015-16, although this was seen only in rural practices. In both rural and urban practices, there was a significant reduction in-between practice variability in request rates. The mean number of HbA1c requests increased from 1.9 to 3.0 per practice patient with diabetes. Variability in HbA1c request rates increased from 23.8% to 36.6%. At all considered time points, test request rates and variability were higher in rural than in urban areas.\n\nConclusionsThe intervention was associated with a reduction in both the volume and between practice variability of profile test requests, with differences noted between rural and urban practices. The increase in HbA1c requests may reflect a more appropriate rate of diabetes monitoring and also the adoption of HbA1c as a diagnostic test.\n\nStrengths & limitations of the studyO_LIWe assessed the effect of a laboratory demand optimisation intervention both on the value and between GP practice variability in laboratory test requesting.\nC_LIO_LIThe changes in laboratory test requesting were separately evaluated for rural and urban GP practices.\nC_LIO_LIOther factors (GP practice organisation, characteristics of general practitioners) potentially affecting between practice differences in laboratory test ordering were not taken into account due to data unavailability.\nC_LIO_LIThe demand management initiative was not accompanied by the cost-effectiveness analysis.\nC_LIO_LIThe demand optimisation intervention was conducted in a Northern Ireland (NI) Western Health and Social Care Trust and the findings have not been independently replicated in any other NI trusts.\nC_LI

pathology↗