Towards monitoring that makes sense : action research design of a planning, learning and accountability system for a sustainable agriculture programme in Eastern Indonesia

This study is an account of an action research process to develop a planning, learning and accountability (PLA) system for the sustainable agriculture chain development programme of VECO (Vredeseilanden Country Office) Indonesia. Many monitoring and evaluation (M&E) processes in development programmes are largely carried out to provide information for funding agencies, to meet external accountability requirements and for symbolic protection. This study generates insights into an integrated, learning-oriented monitoring practice which fosters reflective practice, provides feedback to programme stakeholders about performance, progress and results achieved, facilitates improved accountability, and generates information and knowledge useful for the programme stakeholders to take decisions for improved action. It is argued that M&E systems have the potential, if developed well, to serve as a framework or ‘carrier’ for organisational and institutional learning – an essential requirement to respond to the complex nature of development processes. Outcome mapping is presented as a possible approach to be used as the basis for such a M&E system. This study was underpinned by a socially critical orientation to development (programmes) and by an action research method to guide the PLA system design process. The design process was organized around seven steps - which in themselves were a result of the action research process – including specific steps to ensure a learning-oriented M&E system. Based on the agreed purposes and intended uses of the monitoring and learning process, the resulting PLA system is focused around the organizational spaces and rhythms of VECO Indonesia which are central to sharing, debate, learning and decision-making. In this way, the PLA system becomes integral to the thinking and doing of the organization. It is built on the premise that monitoring does not end with gathering data; it also needs to include a process of understanding and deciding how data can best be used and analysed to strengthen concerted action and facilitate decision-making. It highlights the importance of sense-making – interpreting information to make it usable for action. Furthermore, it incorporates an approach to assess and consciously plan for the creation of the necessary organisational conditions to implement and maintain a learning-oriented M&E system. The study is completed by critical reflection on the relevance of VECO’s new PLA system for planning, learning and accountability, combined with the use of a future scenario technique to generate recommendations and identify critical future directions. Further exploration of ‘intelligent’ information-seeking methods and processes is called for; and a practice which moves beyond intra-organisational monitoring – focusing on VECO’s own monitoring needs – towards a monitoring process that facilitates change based on the viewpoints of, and in collaboration with local actors, i.e., institutional monitoring and learning, is recommended. VECO is encouraged to continue developing a mindset and practice whereby the programme team and partners have the ability to leave the safe zone of pre-determined outcomes and actions, and to make sense of the world as they engage in action

pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity

The plasma membrane H+-ATPase Pma1 and the vacuolar V-ATPase act in close harmony to tightly control pH homeostasis, which is essential for a vast number of physiological processes. As these main two regulators of pH are responsive to the nutritional status of the cell, it seems evident that pH homeostasis acts in conjunction with nutrient-induced signalling pathways. Indeed, both PKA and the TORC1-Sch9 axis influence the proton pumping activity of the V-ATPase and possibly also of Pma1. In addition, it recently became clear that the proton acts as a second messenger to signal glucose availability via the V-ATPase to PKA and TORC1-Sch9. Given the prominent role of nutrient signalling in longevity, it is not surprising that pH homeostasis has been linked to ageing and longevity as well. A first indication is provided by acetic acid, whose uptake by the cell induces toxicity and affects longevity. Secondly, vacuolar acidity has been linked to autophagic processes, including mitophagy. In agreement with this, a decline in vacuolar acidity was shown to induce mitochondrial dysfunction and shorten lifespan. In addition, the asymmetric inheritance of Pma1 has been associated with replicative ageing and this again links to repercussions on vacuolar pH. Taken together, accumulating evidence indicates that pH homeostasis plays a prominent role in the determination of ageing and longevity, thereby providing new perspectives and avenues to explore the underlying molecular mechanisms.Support via the research grants G.0694.13, G.0A63.15 and SBO-S006617N. We also thank KU Leuven for support by granting the C14/17/063 projectinfo:eu-repo/semantics/publishedVersio

The role of Sch9 and the V-ATPase in the adaptation response to acetic acid and the consequences for growth and chronological lifespan

Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9∆ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan

Decoding genetic markers of multiple phenotypic layers through biologically constrained Genome-to-Phenome Bayesian Sparse Regression

International audienceThe applicability of multivariate approaches for the joint analysis of genomics and phenomics information is currently limited by the lack of scalability, and by the difficulty of interpreting the related findings from a biological perspective. To tackle these limitations, we present Bayesian Genome-to-Phenome Sparse Regression (G2PSR), a novel multivariate regression method based on sparse SNP-gene constraints. The statistical framework of G2PSR is based on a Bayesian neural network, were constraints on SNPs-genes associations are integrated by incorporating a priori knowledge linking variants to their respective genes, to then reconstruct the phenotypic data in the output layer. Interpretability is promoted by inducing sparsity on the genes through variational dropout, allowing to estimate the uncertainty associated with each gene, and related SNPs, in the reconstruction task. Ultimately, G2PSR is conceived to prevent multiple testing correction and to assess the combined effect of SNPs, thus increasing the statistical power in detecting genome-to-phenome associations. The effectiveness of G2P was demonstrated on synthetic and real data, with respect to state-of-the-art methods based on group-wise sparsity constraints. The application on real data consisted in an imaging-genetics analysis on the Alzheimer's Disease Neuroimaging Initiative data, relating SNPS from more than 3500 genes to clinical and multi-variate brain volumetric information. The experimental results show that our method can provide accurate selection of relevant genes in dataset with large SNPs-to-samples ratio, thus overcoming the main limitations of current genome-to-phenome association methods

Clustering with feature selection using alternating minimization. Application to computational biology

This paper deals with unsupervised clustering with feature selection. The problem is to estimate both labels and a sparse projection matrix of weights. To address this combina-torial non-convex problem maintaining a strict control on the sparsity of the matrix of weights, we propose an alternating minimization of the Frobenius norm criterion. We provide a new efficient algorithm named K-sparse which alternates k-means with projection-gradient minimization. The projection-gradient step is a method of splitting type, with exact projection on the ℓ 1 ball to promote sparsity. The convergence of the gradient-projection step is addressed, and a preliminary analysis of the alternating minimization is made. The Frobenius norm criterion converges as the number of iterates in Algorithm K-sparse goes to infinity. Experiments on Single Cell RNA sequencing datasets show that our method significantly improves the results of PCA k-means, spectral clustering, SIMLR, and Sparcl methods. The complexity of K-sparse is linear in the number of samples (cells), so that the method scales up to large datasets. Finally, we extend K-sparse to supervised classification

Unconventional surface plasmon resonance signals reveal quantitative inhibition of transcriptional repressor EthR by synthetic ligands

International audienceEthR is a mycobacterial repressor that limits the bioactivation of ethionamide, a commonly used anti-tuberculosis second-line drug. Several efforts have been deployed to identify EthR inhibitors abolishing the DNA-binding activity of the repressor. This led to the demonstration that stimulating the bioactivation of ETH through EthR inhibition could be an alternative way to fight Mycobacterium tuberculosis. We propose a new SPR methodology to study the affinity between inhibitors and EthR. Interestingly, the binding between inhibitors and immobilized EthR produced a dose dependent negative SPR signal. We demonstrated that this signal reveals the affinity of the small molecules for the repressor. The affinity constants (KD) correlated with their capacity to inhibit the binding of EthR to DNA. We hypothesize that conformational changes of EthR during ligand interaction could be responsible for this SPR signal. Practically, this unconventional result open perspectives to the development of SPR assay that would at the same time tough on the structural changes of the target upon binding with an inhibitor and on the binding constant of this interaction

Estrogens reduce the expression of YKL-40 in the retina: Implications for eye and joint diseases

PURPOSE. To identify modifications in the gene expression profile of the ocular posterior segment in ovariectomized (OVX) mice with and without substitutive estradiol therapy and to select differentially expressed genes that could be relevant to the natural history of human age-related macular degeneration (AMD). METHODS. Chorioretinal tissues from two groups of 25 treated and untreated OVX mice were analyzed by using cDNA array technology. The expression level of selected genes was confirmed in triplicate by RT-PCR and related to the estrogenic status of the animals. Expression of the YKL-40 gene was further investigated in intact or diseased human retinas and in a murine model of experimental choroidal neovascularization (CNV), using laser pressure catapulting. RESULTS. Of the approximately, 10,000 genes screened, only YKL-40 expression was significantly downregulated by 17-beta-estradiol. YKL-40 was expressed in intact human neural retina and in the RPE. The expression of YKL-40 was upregulated in experimental CNV and in neovascular membranes extracted from patients affected by the exudative form of AMD. CONCLUSIONS. These observations indicate that YKL-40 expression in the retina is modulated by serum levels of estradiol. This protein could be relevant to the development of AMD and is also a new mediator to take into account when evaluating the broad consequences of hormonal replacement therapy

Eight further individuals with intellectual disability and epilepsy carrying bi-allelic CNTNAP2 aberrations allow delineation of the mutational and phenotypic spectrum

Background Heterozygous copy number variants (CNVs) or sequence variants in the contactin-associated protein 2 gene CNTNAP2 have been discussed as risk factors for a wide spectrum of neurodevelopmental and neuropsychiatric disorders. Bi-allelic aberrations in this gene are causative for an autosomal-recessive disorder with epilepsy, severe intellectual disability (ID) and cortical dysplasia (CDFES). As the number of reported individuals is still limited, we aimed at a further characterisation of the full mutational and clinical spectrum. Methods Targeted sequencing, chromosomal microarray analysis or multigene panel sequencing was performed in individuals with severe ID and epilepsy. Results We identified homozygous mutations, compound heterozygous CNVs or CNVs and mutations in CNTNAP2 in eight individuals from six unrelated families. All aberrations were inherited from healthy, heterozygous parents and are predicted to be deleterious for protein function. Epilepsy occurred in all affected individuals with onset in the first 3.5 years of life. Further common aspects were ID (severe in 6/8), regression of speech development (5/8) and behavioural anomalies (7/8). Interestingly, cognitive impairment in one of two affected brothers was, in comparison, relatively mild with good speech and simple writing abilities. Cortical dysplasia that was previously reported in CDFES was not present in MRIs of six individuals and only suspected in one. Conclusions By identifying novel homozygous or compound heterozygous, deleterious CNVs and mutations in eight individuals from six unrelated families with moderate-to-severe ID, early onset epilepsy and behavioural anomalies, we considerably broaden the mutational and clinical spectrum associated with bi-allelic aberrations in CNTNAP2

MYH7 p.(Arg1712Gln) is pathogenic founder variant causing hypertrophic cardiomyopathy with overall relatively delayed onset

Introduction: The MYH7 c.5135G &gt; A p.(Arg1712Gln) variant has been identified in several patients worldwide and is classified as pathogenic in the ClinVar database. We aimed to delineate its associated phenotype and evaluate a potential founder effect.Methods: We retrospectively collected clinical and genetic data of 22 probands and 74 family members from an international cohort.Results: In total, 53 individuals carried the MYH7 p.(Arg1712Gln) variant, of whom 38 (72%) were diagnosed with hypertrophic cardiomyopathy (HCM). Mean age at HCM diagnosis was 48.8 years (standard deviation: 18.1; range: 8–74). The clinical presentation ranged from asymptomatic HCM to arrhythmias (atrial fibrillation and malignant ventricular arrhythmias). Aborted sudden cardiac death (SCD) leading to the diagnosis of HCM occurred in one proband at the age of 68 years, and a family history of SCD was reported by 39% (5/13) probands. Neither heart failure deaths nor heart transplants were reported. Women had a generally later-onset disease, with 14% of female carriers diagnosed with HCM at age 50 years compared with 54% of male carriers. In both sexes, the disease was fully penetrant by age 75 years. Haplotypes were reconstructed for 35 patients and showed a founder effect in a subset of patients.Conclusion: MYH7 p.(Arg1712Gln) is a pathogenic founder variant with a consistent HCM phenotype that may present with delayed penetrance. This suggested that clinical follow-up should be pursued after the seventh decade in healthy carriers and that longer intervals between screening may be justified in healthy women &lt; 30 years.</p