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Biology subjects

Rossi, N.

Publications and source records attributed to Rossi, N..

15 recordsLinked to original sources

Behavioural flexibility masks delayed costs of environmental instability

Environmental predictability influences the value of information acquired through experience, yet relatively little is known about how instability in resource characteristics influences behavioural organisation during foraging. We tested whether repeated changes in floral orientation, a manipulation of environmental predictability, affect pollen foraging in bumblebees (Bombus terrestris) by exposing naive workers to either stable floral conditions (single flower orientation) or repeated inter-trial changes in flower orientation (three alternating flower orientations), under constant resource availability. We quantified pollen collection, foraging efficiency, revisitation behaviour, floral coverage and sonication behaviour across three successive foraging trials of either constant or variable flower orientation, before assessing performance in a common post-treatment preference test in which bees were offered all three flower orientations and higher pollen rewards. Environmental instability altered the organisation of foraging behaviour. Bees exposed to unstable floral conditions progressively reduced flower revisitation behaviour and were less likely to perform sonication, although floral coverage, defined as the number of unique flowers visited, remained unchanged. Contrary to our predictions, instability had only weak immediate effects on pollen acquisition and foraging efficiency compared to bees tested under stable conditions. However, previous exposure to instability generated carry-over effects in the common post-treatment preference test. Bees previously exposed to unstable conditions were significantly less likely to return with pollen and consequently collected less pollen overall than bees previously exposed to stable conditions. Our results demonstrate that environmental instability can influence pollen foraging in ways that are not captured by immediate measures of performance. Although behavioural adjustments appeared to buffer short-term consequences during repeated foraging trials, carry-over effects were evident when bees were later tested in a common high-reward, multi-orientation floral array. These findings highlight the importance of considering both behavioural flexibility and carry-over effects when evaluating how organisms respond to changing environments.

animal behavior and cognition↗

Warming limits energetic investment in feeding and post-feeding metabolism in bumblebees

Environmental warming is generally expected to increase metabolic demand in ectotherms. However, facultatively endothermic insects such as bumblebees regulate body temperature and may reduce thermogenic investment under warm conditions, potentially altering physiological performance and responses to climate change. We combined flow-through respirometry and infrared thermography to test how elevated ambient temperature (25 vs 35{degrees}C) affects feeding energetics and postprandial metabolism in the bumblebee Bombus terrestris. Bees maintained substantially lower thoracic temperature excess at 35{degrees}C than at 25{degrees}C, both before and during feeding. Feeding metabolic rate was also lower at 35{degrees}C and was strongly positively associated with thoracic temperature excess, indicating that feeding energetics were primarily explained by thermoregulatory state rather than ambient temperature alone. Elevated temperature reduced both the probability and energetic magnitude of specific dynamic action (SDA), including total SDA expenditure, early postprandial metabolism, and peak metabolic amplitude. In contrast, SDA duration and time to peak response showed little temperature dependence. Our results demonstrate that warming can suppress energetic expenditure in facultatively endothermic pollinators by limiting thermogenic investment and postprandial metabolic responses, potentially constraining the energetic flexibility underpinning foraging performance under climate warming.

physiology↗

Long-read cross-platform validation reveals novel repeat features in myotonic dystrophy type 2

The broader application of long-read sequencing (LRS) for repeat expansion characterization in myotonic dystrophy type 2 (DM2) and other repeat expansion disorders (REDs) remains limited by the lack of systematic validation and benchmarking of sequencing results and bioinformatic workflows. Here, we performed an orthogonal cross-platform validation of previously generated Oxford Nanopore Technologies (ONT) data by sequencing the same DNA samples with Pacific Biosciences (PacBio) HiFi following amplification-free targeted enrichment in a cohort of 8 DM2 patients. Despite substantial differences in sequencing chemistry and coverage, the two platforms showed high concordance in repeat size estimation, somatic mosaicism, and repeat architecture. This validation confirmed the presence of the (TCTG)n motif and enabled the identification of a previously unreported (CCCG)n motif at the 3' end of expanded alleles, further highlighting the structural complexity of the CNBP expansion. Through this analysis, we also established a bioinformatic workflow that improved ONT-based repeat characterization, addressing limitations in motif resolution and enabling more accurate analysis of CNBP expansions. Overall, this study provides a validated framework for LRS-based CNBP repeat analysis, supporting the integration of these technologies into routine molecular investigation for DM2 and other REDs.

genomics↗

On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow

Studies focused on bacterial diversity in rivers often face significant limitations. Traditional sampling approaches frequently overlook spatial and temporal variability at the reach scale. Molecular techniques, such as metabarcoding and metagenomics, can partially address this issue by providing deeper insights. However, this approach usually involves highly specialized laboratories and high costs, making large-scale and long-term monitoring of river networks unfeasible in most cases. Thus, we developed a methodology based on remote-controlled boats, allowing the collection of integrated samples in freshwater ecosystems. Combined with a portable laboratory, this approach enabled the development of new surface water monitoring strategies. Here, we describe the operational application of this system for in situ monitoring of bacterioplankton communities across 8 sections of the Ter River (Catalonia, Spain). [To explore its potential, we applied both 16S rRNA gene sequencing using Nanopore technology (MinION) in the field, and shotgun metagenomics using Illumina technology in the laboratory, acknowledging the intrinsic differences between sequencing targets, platforms, and analysis pipelinesMinIONMinION sequencing enabled microbiome characterization and identification of the main bacterial taxa just 72 h after sampling, offering significantly lower costs and reduced manpower requirements. Furthermore, amplification facilitated the full characterization of bacterioplankton diversity along the river, preventing the exclusion of uncommon taxa. While shotgun metagenomics is still necessary for understanding the functional activity of these organisms, our approach provides a cost-effective framework for developing efficient follow-up sampling methodologies.

microbiology↗

First direct quantification of floral handling costs in bees

Floral handling can be energetically costly for bees, yet these costs are rarely measured. We provide the first direct quantification of the metabolic cost of floral buzzing in bumblebees and evaluate its ecological significance. Using flow-through respirometry synchronised with laser vibrometry, we measured carbon dioxide production during buzzing by Bombus terrestris and compared it with flight take-off, which is powered by the same thoracic muscles. Buzzing required high muscular effort, with [~]0.10 J per event and mass-specific power [~]293 W kg-{superscript 1}, and overall costs comparable to take-off because buzzing bouts are longer even though the metabolic rate is lower. Absolute metabolic rate increased with body mass, whereas intertegular span did not, implying that transient load rather than structural size better explains energetic demand in short, high-intensity behaviours. Metabolic traits were repeatable within individuals, and colony identity explained additional variance, consistent with genetic or shared environmental effects. Converting costs to nectar equivalents showed that buzzing required slightly more nectar than take-off and that requirements rose as nectar sugar concentration declined. We conclude that floral buzzing is a major, previously unquantified component of bee energy budgets that is likely to shape nectar supplementation, flower sequencing, and plant-pollinator interaction strength.

animal behavior and cognition↗

Male bumblebees adapt foraging to environmental conditions to sustain mate-seeking efforts

Male bees navigate complex trade-offs between energy acquisition and reproductive signalling, yet their movement strategies remain understudied. Unlike workers that optimise foraging to support the colony, males forage independently to collect nectar and deposit sex pheromones on selected plants. Using high-resolution 3D tracking in an indoor flight cage, we investigated how the spatial arrangement of nectar and scent-marking sites, along with nectar availability, influence male movement patterns. We manipulated the distribution of feeders (artificial flowers) and scent-marking locations (branches), and varied nectar delivery rates, to assess effects on foraging, scent-marking, and patrolling. Males responded strongly to spatial structure: in clumped arrays with evenly spaced resources, movements between consecutive visits were shorter and more localised, while in dispersed arrays with irregular spacing, transitions were longer and more variable. The combination of dispersed spacing and low nectar availability imposed the highest foraging demands, resulting in fewer feeding events and reduced total feeding time. Despite these increased costs, males maintained consistent investment in reproductive behaviours, suggesting a prioritisation of mate-seeking over energy gain. Rather than reducing signalling, males adjusted their foraging strategy--favouring fewer but prolonged feeding bouts when nectar availability allowed. These findings reveal a unidirectional behavioural adjustment, in which foraging is modulated to sustain reproductive effort, and show how spatial resource structure and nectar availability together shape movement decisions in male pollinators. LAY SUMMARYMale bumblebees keep searching for mates even when food is scarce, adjusting how they forage to conserve energy. Using 3D tracking in a controlled environment, we found that males reduce foraging effort but maintain reproductive behaviours. This shows how animals balance survival and reproduction in changing environments, offering new insights into pollinator behaviour and resilience.

animal behavior and cognition↗

From Photoperiod Thresholds to Photoperiod sensitivity: Dual Strategies for Cost-Effective Speed Breeding and Climate-Ready Barley

Yield and the duration of the growing season are closely linked. Climate change may shorten growing seasons in certain European regions, and reducing the time to flowering could be an effective strategy to mitigate its effects. Therefore, exploring allelic combinations shape flowering time, is needed. Additionally, speed breeding (SB), characterized by extended photoperiods to accelerate generation time, can be energy-intensive, and the shortest day length needed to induce rapid flowering remains unknown. We present the first integrated study of how allelic variation at three key flowering time genes, PPD-H1, ELF3 and PHYC, modulates three parameters of the photoperiod response model: threshold photoperiod, photoperiod sensitivity, and intrinsic earliness. We recorded flowering under lengths of 16-24h in Near Isogenic Lines carrying PhyC-e or PhyC-I allele within ppd-H1 background, and in lines from HEB-25 combining wild and domesticated alleles of ELF3 and PPD-H1. The ELF3 allele in ppd-H1 background reduced intrinsic earliness, whereas PhyC-e reduced photoperiod sensitivity, opening opportunities for climate change adaptation. Remarkably, ppd-H1 lines flowered at a 20-h threshold, whereas Ppd-H1 lines showed no response, consequently we propose new SB photoperiods at 20 and 16h depending on PPD-H1 background. These photoperiods lower energy costs compared to the current 22h standard. HighlightsBy studying barley key photoperiod response genes, our results support energy-efficient speed breeding and the development of climate-resilient varieties through targeted genetic control of flowering time.

plant biology↗

Investigating the genetic control of plant development under speed breeding conditions

Speed breeding is a powerful tool to accelerate breeding and research programmes by shortening generation time and has been widely adopted for a range of crop species. Despite its success and growing popularity with breeders the genetic basis of plant development under speed breeding remains unknown. In this study, we explored how genotypes respond in terms of developmental advancement under different photoperiod regimes in the context of speed breeding. A subset of the barley HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: 1) Speed Breeding (SB) consisting of 22 hours of light and 2 hours of darkness), and 2) Normal Breeding (NB) consisting of 16 hours of light and 8 hours of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both NB and SB. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesise that this may be related to the dark dependent repression of PPD-H1 by ELF3 which might be more prominent in NB conditions. Furthermore, by comparing development under two contrasting photoperiod regimes, we were able to derive an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimisation of speed breeding protocols particularly when incorporating genetics from wild relatives into breeding programmes and the design of breeding programmes to support the delivery of climate resilient crops.

plant biology↗

A Conservative Approach for Describing Cancer Progression

The field of tumor phylogenetics focuses on studying the differences within cancer cell populations and many efforts are done within the scientific community to build cancer progression models trying to understand the heterogeneity of such diseases. These models are highly dependent on the kind of data used for their construction and, as the experimental technologies evolve, it is of major importance to exploit their peculiarities. In this work we describe a cancer progression model based on Single Cell DNA Sequencing data. When constructing the model, we focus on tailoring the formalism on the specificity of the data, by defining a minimal set of assumptions to reconstruct a flexible DAG structured model, capable of identifying progression beyond the limitation of the infinite site assumption. We provide simulations and analytical results to show the features of our model, test it on real data, show how it can be integrated with other approaches to cope with input noise. Moreover, our framework can be exploited to produce simulated data that follows our theoretical assumptions. Finally, we provide an open source R implementation of our approach that is publicly available on BioConductor.

bioinformatics↗

Preclinical studies for plant-based oral enzyme replacement therapy (Oral-ERT) in Pompe disease knockout mice with transgenic tobacco seeds expressing human GAA (tobrhGAA)

Genetic deficiency of acid -glucosidase (GAA) results in glycogen storage disease type II (GSDII) or Pompe disease (PD) encompassing at least four clinical subtypes of varying severity (infantile; childhood, juvenile and late onset). Our objective is to develop an innovative and affordable approach for enzyme replacement therapy (ERT) via oral administration (Oral-ERT) to maintain a sustained, therapeutic level of enzyme on a daily basis to improve efficacy of treatment and quality of life for people living with Pompe disease. A consensus at a 2019 US Acid Maltase Deficiency (AMDA) conference suggested that a multi-pronged approach including gene therapy, diet, exercise, etc. must be evaluated for a successful treatment of Pompe disease. Tobacco seeds contain the metabolic machinery that is more compatible with mammalian glycosylation-phosphorylation and processing. Previously, we have shown that a lysate from transgenic tobacco seeds expressing human GAA (tobrhGAA) was enzymatically active and can correct enzyme deficiency in cultured PD cells and in adult lymphocytes of Pompe patients and in vivo in disease-relevant tissues in GAA knockout (KO) mice when administered IP. We have extended these pre-clinical studies in PD knockout (KO) mice with ground tobrhGAA seeds that supports proof-of-concept for Oral-ERT for future clinical trials. Briefly in GAA KO mice, Oral-ERT with ground tobrhGAA seeds showed significant reversal of fore-limb and hind-limb muscle weakness, increased motor coordination/balance/strength and mobility, improved spontaneous learning, increased GAA baseline activity in tissues, reduced glycogen in tissues and negible serum titers to GAA. Pharmacokinetics showed maximum serum GAA concentration (Cs) at 8-10 hr and peak urine excretion at 10-12 hr. The tobrhGAA was taken up in PD fibroblast, lymphoid and myoblast cells. Enzyme kinetics compared favorably or superior to placental hGAA, plus alglucosidase alfa or other rhGAAs for Km, Vmax, pH optima, thermal heat stability and IC50 for inhibitors. The tobrhGAA in seeds was extremely stable stored for 15 years at room temperature. NGS-genome sequencing of the tobrhGAA and wild-type plants and RNA expression profiles was performed and will be posted on our website. Thus, Oral-ERT with ground tobrhGAA seeds is an innovative approach that overcomes some of the challenges of alglucosidase alfa-ERT and provides a more effective, safe and significantly less expensive treatment.

genetics↗

Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable

X-chromosome inactivation (XCI) silences one X-chromosome in female cells to balance sex-differences in X-dosage. A subset of X-linked genes escape XCI, but the extent to which this phenomenon occurs and how it varies across tissues and in a population is as yet unclear. In order to characterize the incidence and variability of escape across individuals and tissues, we conducted a large scale transcriptomic study of XCI escape in adipose, skin, lymphoblastoid cell lines (LCLs) and immune cells in 248 twins drawn from a healthy population cohort. We identify 159 X-linked genes with detectable escape, of which 54 genes, including 19 lncRNAs, were not previously known to escape XCI. Across tissues we find a range of tissue-specificity, with 11% of genes escaping XCI constitutively across tissues and 24% demonstrating tissue-restricted escape, including genes with cell-type specific escape between immune cell types (B, T-CD4+, T-CD8+ and NK cells) of the same individual. Escape genes interact with autosomal-encoded proteins and are involved in varied biological processes such as gene regulation. We find substantial variability in escape between individuals. 49% of genes show inter-individual variability in escape, indicating escape from XCI is an under-appreciated source of gene expression differences. We utilized twin models to investigate the role of genetics in variable escape. Overall, monozygotic (MZ) twin pairs share more similar escape than dizygotic twin pairs, indicating that genetic factors underlie differences in escape across individuals. However, we also identify instances of discordant XCI within MZ co-twin pairs, suggesting that environmental factors also influence escape. Thus, XCI escape may be shaped by an interplay of genetic factors with tissue- and cell type-specificity, and environment. These results illuminate an intricate phenotype whose characterization aids understanding the basis of variable trait expressivity in females.

genetics↗

WGA-LP: a pipeline for Whole Genome Assembly of contaminated reads

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSSummaryC_ST_ABSWhole Genome Assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard (Del Angel et al. (2018)) and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-art programs and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads. Availability and ImplementationWGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/). ContactNicolo Rossi, olocin.issor@gmail.com Supplementary informationSupplementary data are available at bioRxiv online.

bioinformatics↗

Interplay between the human gut microbiome and host metabolism

The human gut is inhabited by a complex and metabolically active microbial ecosystem regulating host health. While many studies have focused on the effect of individual microbial taxa, the metabolic potential of the entire gut microbial ecosystem has been largely under-explored. We characterised the gut microbiome of 1,004 twins via whole shotgun metagenomic sequencing (average 39M reads per sample). We observed greater similarity, across unrelated individuals, for functional metabolic pathways (82%) than for taxonomic composition (43%). We conducted a microbiota-wide association study linking both taxonomic information and microbial metabolic pathways with 673 blood and 713 faecal metabolites (Metabolon, Inc.). Metabolic pathways associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species-level results identified less than 3,000 associations, suggesting that coordinated action of multiple taxa is required to affect the metabolome. Finally, we estimated that the microbiome mediated a crosstalk between 71% of faecal and 15% of blood metabolites, highlighting six key species (unclassified Subdoligranulum spp., Faecalibacterium prausnitzii, Roseburia inulinivorans, Methanobrevibacter smithii, Eubacterium rectale, and Akkermansia muciniphila). Because of the large inter-person variability in microbiome composition, our results underline the importance of studying gut microbial metabolic pathways rather than focusing purely on taxonomy to find therapeutic and diagnostic targets.

microbiology↗

Forecasting when cells die during antibiotic exposure using stochastic gene expression

Antibiotic killing does not occur at a single, precise time for all cells within a population. Variability in time to death can be caused by stochastic expression of genes, resulting in differences in endogenous stress-resistance levels between individual cells in a population. This variability can be part of a bet-hedging strategy where cells leverage noise to ensure a subset of the population can tolerate the drug, while decreasing the overall cost of expressing resistance genes. We asked whether single-cell differences in gene expression prior to antibiotic addition were related to cell survival times after antibiotic exposure for a range of genes of diverse function. We quantified the time to death of single cells under antibiotic exposure in combination with expression of reporters. For some reporters, the time to cell death had a strong relationship with the initial expression level of the genes. Reporters that could forecast cell fate included stress response genes, but also genes involved in a variety of other cellular processes like metabolism. Our results highlight the single-cell level non-uniformity of antibiotic killing and also provide examples of key genes where cell-to-cell variation in expression prior to antibiotic exposure is strongly linked to extended durations of antibiotic survival.

systems biology↗