Biology subjects

Martini, A.

Publications and source records attributed to Martini, A..

7 recordsLinked to original sources

bioRxiv2026

Endophytic colonization pathways of Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 in grapevine following stem injection

Endophytic biocontrol agents may contribute to grapevine health, but their ability to establish, persist, and move within woody tissues remains poorly understood. In this study, a stem injection method was developed to introduce Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 into rooted and grafted grapevine plants, and their spatial and temporal colonization patterns were compared with the movement of a dye tracer. The dye tracer moved rapidly through xylem tissues, whereas both microorganisms showed more restricted early distribution. Over time, M71 and SC1 displayed distinct colonization patterns. M71 persisted after injection, but remained localized near the inoculation site, with limited movement toward roots or distal aerial tissues. In grafted plants, M71 recovery depended on the injection site and declined more markedly after rootstock injection than after scion injection. In contrast, SC1 showed broader and more persistent colonization. In rooted cuttings, SC1 was recovered from stem and root tissues up to 56 days post-injection, and in grafted plants it was recovered across the graft union, particularly after scion injection. Microscopy supported internal localization of both microorganisms. GFP-labelled M71 and SC1 hyphae were observed mainly within xylem vessels, and viable microorganisms were recovered from corresponding wood tissues. No contamination was observed in control plants. These results show that beneficial microorganisms can be introduced into grapevine tissues by stem injection and that bacterial and fungal biocontrol agents differ markedly in their internal movement and persistence. IMPORTANCEIntroducing beneficial microorganisms directly into plant tissues could help in establishing protective endophytic populations, but little is known about how such microorganisms move and persist inside grapevine. This study shows that stem injection can deliver Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 into grapevine tissues without visible phytotoxicity. The two microorganisms followed different colonization patterns. M71 remained mostly localized near the injection site, whereas SC1 spread more broadly and persisted in both rooted and grafted plants. These findings provide a basis for developing targeted endophytic biocontrol strategies in grapevine propagation and early plant establishment. This approach may be particularly relevant for grapevine trunk diseases and other vascular disorders, in which pathogens colonize internal woody tissues.

microbiology↗

bioRxiv2026

First detection and characterization of Alongshan virus in Ixodes ricinus ticks from Italy, 2021-2022

Alongshan virus (ALSV) is an emerging tick-borne segmented RNA virus belonging to the Jingmenvirus group and has been reported in humans, ticks, and vertebrates across Asia and Europe. Despite its potential public health relevance, its distribution and genetic diversity remain poorly characterized in several European regions where tick-borne pathogens are endemic. In this study, we developed a specific TaqMan-based real-time RT-PCR assay targeting a conserved region of ALSV segment 2 and used it to investigate the presence of ALSV RNA in Ixodes ricinus ticks collected in northeastern Italy. The assay showed high linearity over a broad dynamic range and no cross-reactivity with related flaviviruses. A total of 212 archival tick samples collected between March 2021 and November 2022 were screened, and 28 samples (13.2%) tested positive for ALSV RNA. Positive ticks were detected in the provinces of Belluno and Vicenza and included individual adult males and nymph pools. A subset of positive samples was further characterized by nested PCR and Sanger sequencing of all four genomic segments. Phylogenetic analyses showed that Italian ALSV sequences clustered within the broader European ALSV diversity and were closely related to strains from Central and Northern Europe, without forming a distinct country-specific lineage. Sequence comparisons suggested purifying selection and revealed differences in predicted structural proteins between European and Chinese strains. These findings provide the first molecular evidence of ALSV circulation in Italy and support further studies to clarify its epidemiology, host range, genetic diversity, and potential clinical relevance. IMPORTANCEAlongshan virus (ALSV) is an emerging tick-borne virus identified in febrile patients in China and subsequently detected in ticks in Russian Federation and several European countries. Although severe disease has not yet been reported in humans, surveillance and elucidation of the virus distribution are essential to assess its pathogenicity and potential public health impact. We developed a specific real-time RT-PCR protocol and detected ALSV in Ixodes ricinus ticks collected in northeastern Italy. Sequence analyses suggested multiple introductions and revealed differences in structural proteins between European and Chinese strains, suggesting potential adaptation and differences in pathogenicity. Since the clinical signs of ALSV infection in humans may overlap with those of tick-borne encephalitis (TBE), differential diagnostic procedures should be developed to improve patient management, particularly in TBE-endemic regions such as northeastern of Italy.

microbiology↗

bioRxiv2026

Chronic acoustic degradation via cochlear implants alters predictive processing of audiovisual speech

This study provides the first neurophysiological evidence of how cochlear implant (CI) input affects predictive processing during audiovisual language comprehension in deaf individuals. Using EEG, we compared 18 CI users with 18 normal-hearing (NH) controls during sentence comprehension where final word predictability was determined by high or low semantic constraint (HC vs. LC) of the preceding sentence frame. Between sentence frame and final word, a 800 ms silent gap was introduced. Mouth visibility was manipulated during sentence frames (visible or digitally occluded; V+ vs. V-), while the final words were always presented with the mouth visible. In NH participants, lower-beta power (12-15 Hz) in left frontal and central sensors decreased for HC vs. LC contexts during the pre-target silent gap, but only when the mouths was visible, suggesting active prediction generation. In CI users, this lower beta power decrease was absent. After final word presentation, both groups showed N400 predictability effects, indicating preserved prediction evaluation. However, CI users exhibited extended N400 effects in the V+ condition, suggesting additional processing demands. Across all participants, pre-target beta modulations correlated with language production abilities, supporting prediction-by-production frameworks. Within CI users, poorer audiometric thresholds correlated with larger N400 constraint effects, possibly indicating greater reliance on contextual prediction to compensate for degraded sensory input. These findings demonstrate that CI-mediated perception alters the neural mechanisms of prediction generation. The link between production skills and predictive mechanisms suggests that strengthening expressive language abilities may enhance predictive processing in CI users.

neuroscience↗

bioRxiv2026

Combination Treatment with Intravesical Interferon-Alpha Gene Therapy and Oral Pan-ErbB Receptor Family Blocker Improves Survival in Mice with Bladder Cancer

PurposeIntravesical interferon-alpha (IFN) gene therapy has shown promise in treating BCG-unresponsive non-muscle invasive bladder cancer (NMIBC). Ongoing work in our lab aims to further improve its treatment efficacy by identifying resistance mechanisms and deploying targeted combination treatment strategies. Experimental designWe performed end-tumor RNA-seq analysis of MB49 murine tumors treated with IFN gene therapy, identifying the ErbB pathway as a resistance mechanism. We consequently hypothesized that a combination treatment involving an ErbB pathway blocker and IFN could yield improved outcomes. MB49 cells were treated in vitro with lentiviral IFN (LV-IFN) gene therapy, with/without Afatinib, a pan-ErbB inhibitor, and cell viability and migration assays were performed. Next, in vivo studies were conducted in the syngeneic MB49 orthotopic murine bladder cancer model. The mice were randomized into 5 treatment groups (n=10 each): saline (Ctrl), LV-Ctrl, oral Afatinib monotherapy, intravesical LV-IFN monotherapy, and the experimental intravesical LV-IFN + oral Afatinib combination therapy. Overall survival (OS) and drug toxicity were assessed. ResultsCombination therapy significantly reduced MB49 cell viability in vitro compared to all other treatment conditions (mean relative ATPase activity at 72 h for the combination treatment was 4%, compared to 100%, 26%, and 28% for Ctrl, LV-IFN, and Afatinib, respectively, p<0.001). This additive effect on cell viability appeared to be driven by a combination of early-cytostatic and late-cytolytic effects. The combination treatment also markedly inhibited cell migration (mean migrated cells/10x Boyden chamber assay at 36 h were: 92.3 for the combination therapy and 631.0, 600.4, and 270.3 for Ctrl, LV-IFN, and Afatinib, respectively, p<0.001). Finally, the in vivo studies demonstrated improved OS with combination therapy (median OS was 49 d in the combination group vs 15, 29, and 26 d in Ctrl, LV-IFN, and Afatinib groups, respectively, Log-rank p<0.001). No mice in the combination therapy group died of drug toxicity. ConclusionsOur preliminary findings suggest that the ErbB pathway may serve as a clinically significant resistance mechanism to intravesical IFN gene therapy, and when targeted concurrently, may improve treatment efficacy.

cancer biology↗

bioRxiv2025

Hypoxia-Induced Metabolic Reprogramming and Markings of Cell Fate in Concentric Arterial Hypertrophy

Chronic inhibition of the renin-angiotensin system (RAS), while widely used to treat hypertension, can lead to an underrecognized form of vascular disease marked by concentric arteriolar and arterial hypertrophy (CAAH). Here, using two lineage-traced mouse models of genetic renin deletion and sustained RAS blockade, we uncover a pathogenic cascade initiated by renin-lineage cell fate reprogramming. Loss of endocrine identity and transformation of smooth muscle cells drives a shift toward a fibrotic, inflammatory, and secretory phenotype that remodels the extracellular matrix and promotes vascular thickening and luminal narrowing. Integrated transcriptomic, proteomic, and metabolomic profiling revealed a hypoxia-linked metabolic switch--characterized by succinate accumulation and NAD+ depletion--coupled to Hif activation and disease progression. We identify Cdh13 and collagens (including Col1a1 and Col12a1) as early urinary biomarkers and define a 10-gene molecular signature of CAAH with potential clinical application. These findings establish renin-lineage cell plasticity and metabolic dysfunction as central drivers of CAAH and nominate candidate biomarkers for early detection and therapeutic targeting in RAS-inhibited patients.

physiology↗

bioRxiv2024

The clumped isotope signatures of multiple methanogenesis metabolisms

Methane is a potent greenhouse gas, an important energy source, and a potential biosignature on extraterrestrial planetary bodies. The relative abundances of doubly substituted ("clumped") methane isotopologues (13CH3D and 12CH2D2) offer important information on the sources and sinks of methane. However, the clumped isotope signatures of microbially produced methane from different methanogenic pathways lack a systematic investigation. In this study, we provide a dataset encompassing the relative isotopologue abundances produced by hydrogenotrophic, methylotrophic, acetoclastic, and methoxydotrophic methanogenesis. We find that a statistical "combinatorial effect" generates significant differences in 12CH2D2 compositions between hydrogenotrophic methanogenesis and other pathways. The thermodynamic drive of methanogenic reactions and phylogenetic affiliation may also influence the isotope compositions of methane. Our study provides new experimental constraints on the isotope signatures of different microbial methanogenic pathways, and evidence of the mechanisms responsible for the observed differences. TeaserA novel stable isotope tool to track and differentiate sources of biological methane.

microbiology↗

bioRxiv2021

immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires

Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. To date, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency, and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (i) reproducing a large-scale study on immune state prediction, (ii) developing, integrating, and applying a novel method for antigen specificity prediction, and (iii) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

bioinformatics↗