Biology subjects

Martini, D.

Publications and source records attributed to Martini, D..

3 recordsLinked to original sources

bioRxiv2026

A Standardized Methodology for FAIRness Assessment and Multi-Dimensional Scoring in Agrosystem Research Data Infrastructures

The NFDI-consortium FAIRagro has established a systematic framework for evaluating the FAIRness of Research Data Infrastructures (RDI) within the German agrosystem research landscape. While FAIR principles are widely accepted, their practical implementation by RDIs remains challenging. By operationalizing the FAIR principles into a reproducible multi-dimensional scoring methodology, this initiative addresses the critical need for a transparent and citable benchmark of RDIs that moves beyond simple compliance. This paper details the underlying assessment criteria, comprising 20 aggregated core metrics, the iterative community-driven validation process, and the integration of these metrics into the FAIRagro Search Hub. This framework evaluates RDIs, like repositories or databases, instead of sampling hosted data sets, across the four distinct categories of FAIR independently, yielding granular, pillar-specific ratings. Unlike aggregate scoring models, which can inadvertently mask technical deficiencies by averaging performance across categories, this multi-dimensional approach ensures that a repositorys distinct strengths and bottlenecks remain fully visible. Our findings demonstrate that standardized scoring not only clarifies data accessibility for users but also highlights specific operational gaps, allowing repository providers to identify precisely where the service implementation can be enhanced. By establishing this data-driven service in the agronomy domain, we provide a scalable template for the broader NFDI and EOSC ecosystems to foster a culture of excellence in research data stewardship.

bioinformatics↗

bioRxiv2024

Ibudilast Protects Retinal Bipolar Cells from Excitotoxic Retinal Damage and Activates the mTOR Pathway

Ibudilast, an inhibitor of macrophage migration inhibitory factor (MIF) and phosphodiesterase (PDE), has been recently shown to have neuroprotective effects in a variety of neurologic diseases. We utilize a chick excitotoxic retinal damage model to investigate ibudilasts potential to protect retinal neurons. Using single cell RNA-sequencing (scRNA-seq), we find that MIF, putative MIF receptors CD74 and CD44, and several PDEs are upregulated in different retinal cells during damage. Intravitreal ibudilast is well tolerated in the eye and causes no evidence of toxicity. Ibudilast effectively protects neurons in the inner nuclear layer from NMDA-induced cell death, restores retinal layer thickness on spectral domain optical coherence tomography, and preserves retinal neuron function, particularly for the ON bipolar cells, as assessed by electroretinography. PDE inhibition seems essential for ibudilasts neuroprotection, as AV1013, the analogue that lacks PDE inhibitor activity, is ineffective. scRNA-seq analysis reveals upregulation of multiple signaling pathways, including mTOR, in damaged Muller glia (MG) with ibudilast treatment compared to AV1013. Components of mTORC1 and mTORC2 are upregulated in both bipolar cells and MG with ibudilast. The mTOR inhibitor rapamycin blocked accumulation of pS6 but did not reduce TUNEL positive dying cells. Additionally, through ligand-receptor interaction analysis, crosstalk between bipolar cells and MG may be important for neuroprotection. We have identified several paracrine signaling pathways that are known to contribute to cell survival and neuroprotection and might play essential roles in ibudilast function. These findings highlight ibudilasts potential to protect inner retinal neurons during damage and show promise for future clinical translation. Graphical AbstractO_ST_ABSMain PointsC_ST_ABS- Ibudilast, a MIF and PDE inhibitor, preserves the form and function of the retina, especially bipolar cells, during excitotoxic damage - Ibudilast upregulates multiple signaling pathways, including mTOR, in damaged Muller glia and bipolar cells O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/585556v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@18d9916org.highwire.dtl.DTLVardef@13db1b2org.highwire.dtl.DTLVardef@15d3d8dorg.highwire.dtl.DTLVardef@742b0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Genomic sequencing confirms absence of introgression despite past hybridisation in a critically endangered bird

Genetic swamping resulting from interspecific hybridisation can increase extinction risk for threatened species. The development of high-throughput and reduced-representation genomic sequencing and analyses to generate large numbers of high resolution genomic markers has the potential to reveal introgression previously undetected using small numbers of genetic markers. However, few studies to date have implemented genomic tools to assess the extent of interspecific hybridisation in threatened species. Here we investigate the utility of genome-wide single nucleotide polymorphisms (SNPs) to detect introgression resulting from past interspecific hybridisation in one of the worlds rarest birds. Anthropogenic impacts have resulted in hybridisation and subsequent backcrossing of the critically endangered Aotearoa New Zealand endemic kak[i] (black stilts; Himantopus novaezelandiae) with the non-threatened self-introduced congeneric poaka (Aotearoa New Zealand population of pied stilts, Himantopus himantopus leucocephalus), yet genetic analyses with a limited set of microsatellite markers revealed no evidence of introgression of poaka genetic material in kak[i], excluding one individual. We use genomic data for [~]63% of the wild adult kak[i] population to reassess the extent of introgression resulting from hybridisation between kak[i] and poaka. Consistent with previous genetic analyses, we detected no introgression from poaka into kak[i]. These collective results indicate that, for kak[i], existing microsatellite markers provide a robust, cost-effective approach to detect cryptic hybrids. Further, for well-differentiated species, the use of genomic markers may not be required to detect admixed individuals.

genomics↗