Biology subjects

Palumbo, F.

Publications and source records attributed to Palumbo, F..

8 recordsLinked to original sources

bioRxiv2026

The BUD13 splicing regulator: transcript structure and expression in ovules of sexual and apomictic Paspalum notatum

Background and AimsPaspalum notatum reproduces through either sexuality or apomixis, two pathways that may coexist within the same individual and are regulated by interconnected molecular networks responsive to environmental cues. Here, we characterized the transcript structure and expression of BUD SITE SELECTION PROTEIN 13 (BUD13), a component of the RES spliceosomal complex previously reported as differentially expressed in florets of sexual and apomictic plants, as a first step toward testing its involvement in the molecular regulation of the apomixis-sexuality switch. MethodsPreviously generated floral and leaf transcriptomes from sexual and apomictic Paspalum notatum plants, including Oxford Nanopore long-read data, were mined to characterize BUD13 transcript structure and expression. Phylogenetic analyses and in silico mapping were conducted to infer evolutionary relationships and determine the origin of the transcripts. Differential expression was validated by RT-qPCR, while in situ hybridization was used to reveal cell-specific ovule expression patterns. Key resultsBUD13 is expressed in Paspalum notatum florets as a truncated isoform (SHORT) encoding a small protein lacking part of the herpes simplex virus regulatory protein (ICP4) domain. Two SHORT transcripts, SHORT1 and SHORT2, with different 5' untranslated region (UTR) regions, were identified in flowers. SHORT1 was consistently upregulated in apomictic ovules from premeiosis to anthesis. Both transcripts originated from a single genomic locus located in the subtelomeric region of the short arm of chromosome 6. SHORT isoforms with variable structures were detected in other monocots. In situ hybridization showed that, whereas BUD13 was expressed throughout sexual ovules, expression was absent from the female germline of apomictic ovules. A consistent expression was observed in somatic proembryos of aposporous embryo sacs. ConclusionsOur findings reveal structural, spatial and temporal divergence in BUD13 expression between sexual and apomictic reproductive programs, providing new insights into the molecular regulation of asexual seed formation.

plant biology↗

bioRxiv2026

DNA Traces on the Shroud of Turin: Metagenomics of the 1978 Official Sample Collection

This research provides original insights into the diversity of DNA extracted from samples collected in 1978 from the Turin Shroud, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. Several human mitochondrial DNA (mtDNA) lineages were identified, including K1a1b1a, which matches the 1978 official collectors mitogenome, H2a2 (i.e. the lineage of the mtDNA reference sequence rRCS), H1b, which is common in Western Eurasia, and H33, which is prevalent in the Near East and frequent among the Druze. Moreover, the reconstructed microbiome of the Shroud reveals a rich tapestry of multiple microbes commonly found on the human epidermis, as well as archaeal communities adapted to high salinity, and fungi including molds. This is indicative of the Shrouds preservation conditions over the centuries. Additionally, the presence of abundant Mediterranean endemic red coral, various cultivated plants (e.g. carrot, wheat, corn, bananas, and peanuts) and domesticated animals (e.g. cattle, pigs, chickens, dogs, and cats) provide a fascinating glimpse into the diverse biological sources of the contaminants that have accumulated on the Turin Shroud over time. Finally, radiocarbon dating of two distinct threads collected from the reliquary provides evidence of their use to repair the Shroud in the years 1534 and 1694 of the Common Era (CE). Significance statementAn in-depth metagenomic analysis was conducted on several linen strands collected from different areas of the body image of the Man of the Shroud during the official sampling in 1978. Our analyses revealed several human mtDNA lineages, including one common in Western Eurasia and another prevalent in the Near East. Additionally, the diversity of animal and plant species identified details the significant environmental contamination of the Shroud that likely occurred in recent centuries, particularly following the voyages of Marco Polo and Christopher Columbus. Radiocarbon dating of two distinct textile residuals from the Shrouds reliquary indicated a time range between 1451 and 1800 CE, overlapping with the period of its repair interventions.

genomics↗

bioRxiv2026

SABER: A Multiparental Tomato Population Leveraging Wild Relative Diversity for High-Resolution QTL Mapping

The narrow genetic base of cultivated tomato (Solanum lycopersicum L.) represents a major constraint on crop improvement, necessitating the exploitation of wild relatives to broaden allelic diversity. Here we present SABER (Solanum lycopersicum Allele Biodiversity Enriched Resources), a novel eight-founder Multiparent Advanced Generation Intercross (MAGIC) population that, for the first time, incorporates the Galapagos wild relative Solanum cheesmaniae as a founder alongside seven elite S. lycopersicum lines. Following a structured crossing scheme and Single Seed Descent advancement, F6 recombinant inbred lines were genotyped at 5,850 high-confidence SNP markers using Single Primer Enrichment Technology (SPET). Population structure analyses confirmed low residual heterozygosity, limited substructure among offspring, and successful introgression of S. cheesmaniae alleles across all twelve chromosomes. Mapping performance was validated through three Mendelian traits with known genetic determinants, all of which resolved to genomic positions consistent with the literature. QTL mapping for quantitative agronomic traits identified known loci for fruit epicarp and flesh color, and two novel QTL for days to flowering, number of leaves before flowering, and soluble solids content. Together, these results demonstrate that SABER is a powerful and reliable platform for high-resolution QTL mapping and candidate gene discovery, and establish a replicable framework for integrating wild germplasm into multiparental tomato breeding resources

plant biology↗

bioRxiv2026

GRASP: A PLANT TRANSFORMATION-INDEPENDENT CRISPR-BASED SYSTEM FOR AFFINITY PURIFICATION OF SPECIFIC CHROMATIN LOCI

Chromatin organization regulates genome stability and gene expression by controlling DNA accessibility to transcription factors and regulatory complexes. DNA-protein interactions are commonly investigated using chromatin immunoprecipitation (ChIP), which relies on specific antibodies often involving technically demanding protocols. CRISPR-Cas technologies have enabled sequence-specific targeting of genomic loci using catalytically inactive Cas9 (dCas9), but most CRISPR-based chromatin capture approaches in plants require transient or stable transformation to express the CRISPR machinery, limiting their applicability across species, tissues and physiological contexts. Here, we present GRASP (Genomic Region Affinity Sequestration by CRISPR-Purification), a transformation-independent strategy for sequence-specific chromatin isolation operating directly on purified plant nuclei. In GRASP, dCas9-gRNA ribonucleoprotein complexes are used to capture predefined genomic regions from chromatin under native conditions, bypassing the need for transgene expression. Using grapevine and tomato as model systems, we demonstrate efficient and highly specific enrichment of target loci, including telomeric repeats as well as low-copy and single-copy genomic regions, with qPCR and NGS validation. These results establish GRASP as a robust and broadly applicable platform for locus-specific chromatin isolation in plants. Beyond sequence-specific DNA isolation, GRASP establishes a versatile platform for potential downstream analyses of locus-associated chromatin components, including protein complexes, distal DNA-DNA interactions and chromatin-associated RNAs, providing new opportunities to investigate regulatory architecture in plant genomes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/712347v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1d63d52org.highwire.dtl.DTLVardef@53e7f3org.highwire.dtl.DTLVardef@a11b4eorg.highwire.dtl.DTLVardef@107c94a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Topographically organized dorsal raphe activity modulates forebrain sensory-motor computations and adaptive behaviors.

The dorsal raphe nucleus (DRN) plays an important role in shaping a wide range of behaviors, including mood, motivation, appetite, sleep, and social interactions. Reflecting these diverse roles, the DRN is composed of molecularly distinct and topographically organized groups of neurons that target specific regions of the forebrain. Despite these insights, fundamental questions remain regarding how DRN neurons process sensory information, what do DRN communicate to forebrain, and the role of DRN inputs in forebrain computations and animal behavior. To address these questions, we investigated the spatiotemporal activity patterns of DRN neurons, along with DRN axons and their targets in the juvenile zebrafish forebrain. Our findings revealed a remarkable topographic organization of ongoing activity and sensory-motor responses within the DRN. We discovered that a large fraction of DRN neurons are primarily driven by animals locomotor activity. We also observed that an anterior group of DRN neurons, marked by Gad1, exhibited distinct activity patterns during rest, locomotor activity and sensory stimulation. DRN axons broadly innervating the forebrain exhibit topographically organized excitation and inhibition in response to sensory stimulation and motor activity. Notably, we observed significant and rapid covariation between the activity of DRN axons and nearby forebrain neurons. Chemogenetic ablation of the DRN led to a marked reduction in the synchrony and sensory-motor responses across forebrain neurons, accompanied by significant deficits in adaptive behaviors. Collectively, our findings revealed the functional diversity of DRN neurons and their role in transmitting sensory and locomotor signals via topographically organized projections, which can regulate forebrain activity and play a crucial role in modulating animal behavior.

neuroscience↗

bioRxiv2019

Investigating olfactory behaviors in adult zebrafish

Odor-driven behaviors such as feeding, mating and predator avoidance are crucial for animal survival. While the zebrafish olfactory circuitry is well understood, a comprehensive description of odor-driven behaviors is needed to better relate olfactory computations to animal responses. Here, we used a medium-throughput setup to measure the swimming trajectories of 10 zebrafish in response to 17 ecologically relevant odors. By selecting appropriate locomotor metrics, we constructed ethograms systematically describing odor-induced changes in the swimming trajectory. We found that fish reacted to most odorants, using different behavioral programs and that combination of few relevant behavioral metrics enabled to capture most of the variance in these innate odor responses. We observed that monomolecular odors in similar chemical categories were weakly clustered based on the behavioral responses, likely because natural odors elicited stronger reactions than the monomolecular odors. Finally, we uncovered a previously undescribed intra and inter-individual variability of olfactory behaviors and suggest a small set of odors that elicit robust responses. In conclusion, our setup and results will be useful resources for future studies interested in characterizing olfactory responses in aquatic animals.

animal behavior and cognition↗

bioRxiv2019

Detecting behavioral patterns for diagnosis and rehabilitation of visual neglect: a technology-enhanced version of the Baking Tray Task

AO_SCPLOWBSTRACTC_SCPLOWVisual neglect is a frequent and disabling consequence of right brain damage. Traditional paper-and- pencil tests of neglect have limitations in sensitivity and ecological validity. The Baking Tray Task (BTT), instead, approaches real-life situations, because it requires participants to place 16 physical objects on a board. The number of objects placed on the left and right portions of the board provides a clinical index of visual neglect. Here we present E-TAN, a technology-enhanced platform which allows patients to perform an enhanced version of the BTT (E-BTT). This platform automatically determines the object locations on the board, and also records the sequence and timing of their placement. We used E-BTT to test 9 patients with right hemisphere damage, and compared their performance with that obtained by 115 healthy participants. To this end, we developed a new method of analysis of participants performance, based on the use of the convex hull described by the objects on the board. This measure provides an estimate of the portion of space processed by each participant, and can effectively discriminate neglect patients from patients without neglect. E-TAN allows clinicians to assess visuospatial performance by using a convenient, fast, and relatively automatized procedure, that patients can even perform at home to follow-up the effects of rehabilitation.

neuroscience↗

bioRxiv2019

Zebrafish dorsal habenula is required for updating learned behaviors

Operant conditioning requires multiple cognitive processes, such as learning, prediction of potential outcomes and decision making. It is less clear how interactions of these processes lead to the behavioral adaptations that allow animals to cope with a changing environment. We showed that juvenile zebrafish can perform conditioned place avoidance learning, with an improving performance across development. Ablation of the dorsolateral habenula (dlHb), a brain region involved in associative learning and prediction of outcomes, led to an unexpected improvement in performance and delayed memory extinction. Interestingly, while the control animals exhibited rapid adaptation to a changing learning rule, dlHb ablated animals failed to adapt. Altogether, our results show that the dlHb plays a central role in switching animals strategies while integrating new evidence with prior experience.

neuroscience↗