Biology subjects

Aiese Cigliano, R.

Publications and source records attributed to Aiese Cigliano, R..

7 recordsLinked to original sources

bioRxiv2025

ARABIDOPSIS Bsister and SEEDSTICK MADS-box transcription factors modulate maternal nutrient flow for seed development in Arabidopsis

Successful seed development in angiosperms depends on the coordinated transport and allocation of sugars from maternal tissues to the developing embryo and endosperm. In Arabidopsis thaliana, ovules function as carbohydrate sink organs, accumulating starch in both gametophytic and sporophytic domains prior to fertilization. This stored starch is later mobilized to support early embryogenesis. Despite extensive knowledge of starch metabolism in photosynthetic tissues, the regulatory mechanisms governing sugar transport in reproductive organs remain poorly understood. Recent studies have identified fertilization-dependent changes in nutrient flow, including callose-mediated modulation of symplastic transport at the phloem unloading site. However, the molecular players orchestrating these transitions are largely unknown. Here, we show that the MIKC MADS domain transcription factors ABS/TT16 and STK play critical roles in regulating maternal nutrient flow during ovule maturation and seed development. We dissect their functional redundancy using omics and genetic approaches, underscoring the importance of different ovule tissues in coordinating sugar transport pathways for post-fertilization development. Our findings reveal a previously underappreciated layer of genetic control over nutrient allocation in reproductive tissues and provide new insights into the metabolic reprogramming required for successful seed formation.

plant biology↗

bioRxiv2022

The virtualome: a computational framework toevaluate microbiome analyses

Microbiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtualomes, virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtualomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information.

bioinformatics↗

bioRxiv2022

Wax worm saliva and the enzymes therein are the key to polyethylene degradation by Galleria mellonella

Plastic degradation by biological systems with re-utilization of the by-products can be the future solution to the global threat of plastic waste accumulation. We report that the saliva of Galleria mellonella larvae (wax worms) is capable of oxidizing and depolymerizing polyethylene (PE), one of the most produced and sturdy polyolefin-derived plastics. This effect is achieved after a few hours exposure at room temperature and physiological conditions (neutral pH). The wax worm saliva can indeed overcome the bottleneck step in PE biodegradation, that is the initial oxidation step. Within the saliva, we identified two enzymes that can reproduce the same effect. This is the first report of enzymes with this capability, opening up the way to new ground-breaking solutions for plastic waste management through bio-recycling/up-cycling.

molecular biology↗

bioRxiv2020

Early Alpine human occupation backdates westward human migration in Late Glacial Europe

The end of the Last Glacial Maximum (LGM) in Europe (~16.5 ka ago) set in motion major changes in human culture and population structure1. In Southern Europe, Early Epigravettian material culture was replaced by Late Epigravettian art and technology about 18-17 ka ago at the beginning of southern Alpine deglaciation, although available genetic evidence from individuals who lived ~14 ka ago2-5 opened up questions on the impact of migrations on this cultural transition only after that date. Here we generate new genomic data from a human mandible uncovered at the Late Epigravettian site of Riparo Tagliente (Veneto, Italy), that we directly dated to 16,980-16,510 cal BP (2{sigma}). This individual, affected by a low-prevalence dental pathology named focal osseous dysplasia, attests that the very emergence of Late Epigravettian material culture in Italy was already associated with migration and genetic replacement of the Gravettian-related ancestry. In doing so, we push back by at least 3,000 years the date of the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bolling/Allerod warming event (~14 ka ago4,6). Our results suggest that demic diffusion from a genetically diverse population may have substantially contributed to cultural changes in LGM and post-LGM Southern Europe, independently from abrupt shifts to warmer and more favourable conditions.

genomics↗

bioRxiv2020

Maintaining oxidized H3 in heterochromatin is required for the oncogenic capacity of triple-negative breast cancer cells

The histone modification of H3 oxidized at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase-like 2 (LOXL2) and is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells. Although H3K4ox has been linked to the maintenance of compacted chromatin, the molecular mechanism underlying this maintenance is unknown. Here we show that H3K4ox is read by the CRL4B complex, leading to the ubiquitination of histone H2A through the E3 ligase RBX1. Finally, interactions between RUVBL1/2 and LOXL2 are involved in the incorporation of the histone variant H2A.Z, which plays an essential role in the mechanism controlling the dynamics of oxidized H3. Maintenance of H3K4ox in chromatin is essential for heterochromatin properties, and disruption of any of the members involved in this pathway blocks the oncogenic properties of TNBC cells.

cancer biology↗

bioRxiv2019

GAIA: an integrated metagenomics suite

Identifying the biological diversity of a microbial population is of fundamental importance due to its implications in industrial processes, environmental studies and clinical applications. Today, there is still an outstanding need to develop new, easy-to-use bioinformatics tools to analyze both amplicon and shotgun metagenomics, including both prokaryotic and eukaryotic organisms, with the highest accuracy and the lowest running time. With the aim of overcoming this need, we introduce GAIA, an online software solution that has been designed to provide users with the maximum information whether it be 16S, 18S, ITS, or shotgun analysis. GAIA is able to obtain a comprehensive and detailed overview at any taxonomic level of microbiomes of different origins: human (e.g. stomach or skin), agricultural and environmental (e.g. land, water or organic waste). By using recently published benchmark datasets from shotgun and 16S experiments we compared GAIA against several available pipelines. Our results show that for shotgun metagenomics, GAIA obtained the highest F-measures at species level above all tested pipelines (CLARK, Kraken, LMAT, BlastMegan, DiamondMegan and NBC). For 16S metagenomics, GAIA also obtained excellent F-measures comparable to QIIME at family level. The overall objective of GAIA is to provide both the academic and industrial sectors with an integrated metagenomics suite that will allow to perform metagenomics data analysis easily, quickly and affordably with the highest accuracy.

bioinformatics↗

bioRxiv2018

Reduction of LOXL2-mediated H3K4 oxidation increases chromatin accessibility and promotes chemosensitivity of triple-negative breast cancer cells

Oxidation of H3 at lysine 4 (H3K4ox) by lysyl oxidase-like 2 (LOXL2) generates an H3 modification with an unknown physiological function. We find that LOXL2 and H3K4ox are higher in triple-negative breast cancer (TNBC) cell lines and patient-derived xenographs (PDXs) than those from other breast cancer subtypes. ChIP-seq revealed that H3K4ox is located primarily in heterochromatin, where it is involved in chromatin compaction. Knocking down LOXL2 reduces H3K4ox levels and causes chromatin decompaction, resulting in a sustained activation of the DNA damage response (DDR) and increased susceptibility to anticancer agents. This critical role that LOXL2 and oxidized H3 play in chromatin compaction and DDR suggests that functionally targeting LOXL2 could be a way to sensitize TNBC cells to conventional therapy.

cancer biology↗