Biology subjects

Zingone, A.

Publications and source records attributed to Zingone, A..

6 recordsLinked to original sources

bioRxiv2024

Patterns and drivers of diatom diversity and abundance in the global ocean

Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity was confirmed, and the most prevalent genera were Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We defined 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection were among the cellular functions in which natural diatom populations invested the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.

ecology↗

bioRxiv2022

Insight into diatoms diversity at two European coastal sites (LTER-MC in the Mediterranean Sea and SOMLIT-Astan in the Western English Channel) using a DNA metabarcoding approach

Diatoms are among the most successful marine eukaryotic phytoplankton groups. Their diversity has been investigated in the worlds oceans through expeditions and observations carried out from the equator to the poles. Traditionally, diatom species have been distinguished based on morphological characters of their frustules, but high-throughput sequencing offers new, high-resolution data that can be used to re-examine spatial and/or temporal patterns of diversity. Here we investigated diatoms genetic diversity using metabarcoding (18S V4 rRNA gene) obtained along the years 2011 to 2013 at two coastal time series stations (SOMLIT-Astan and LTER-MareChiara) installed respectively off Roscoff in the Western English Channel and in the Gulf of Naples in the Mediterranean Sea. Diatom species pools detected were different, which fitted with previous observations and with our expectations, since these stations are installed in two contrasted pelagic habitats (permanently-mixed versus stratified in summer). However, this analysis also shows a pool of common ASVs among which some are persistent and dominant in both sites. The observed synchronous variations in relative read abundances of shared ASVs assigned to Chaetoceros socialis, C. tenuissimus, Cyclotella, Mediolabrus comicus and Leptocylindrus aporus at the two geographically distant sites could indicate that internal controls of growth rate and sexual reproduction, rather that external environmental parameters are at work.

ecology↗

bioRxiv2021

NNAL, a major metabolite of tobacco-specific carcinogen NNK, promotes lung cancer progression through deactivating LKB1 in an isomer-dependent manner

Smoking is associated with worse clinical outcomes for lung cancer patients. Cell-based studies suggest that NNK (a tobacco specific carcinogen) promotes lung cancer progression. Given its short half-life, the physiological relevance of these in vitro results remains elusive. NNAL, a major metabolite of NNK with a similar structure, a chiral center, and a longer half-life, has never been evaluated in cancer cells. In this study, we characterized the effect of NNAL and its enantiomers on cancer progression among a panel of NSCLC cell lines and explored the associated mechanisms. We found that (R)-NNAL promotes cell proliferation, enhances migration, and induces drug resistance while (S)-NNAL has much weaker effects. Mechanistically, (R)-NNAL phosphorylates and deactivates LKB1 via the {beta}-AR signaling in the LKB1 wild type NSCLC cell lines, contributing to the enhanced proliferation, migration, and drug resistance. Of note, NNK exposure also increases the phosphorylation of LKB1 in A/J mice. More importantly, human lung cancer tissues appear to have elevated LKB1 phosphorylation. Our results reveal, for the first time, that NNAL may promote lung cancer progression through LKB1 deactivation in an isomer-dependent manner.

cancer biology↗

bioRxiv2021

Phenological segregation suggests speciation by time in the planktonic diatom Pseudo-nitzschia allochrona sp. nov.

The emergence of new species is poorly understood in marine plankton, where the lack of physical barriers and homogeneous environmental conditions limit spatial and ecological segregation. Here we combine molecular and ecological information from a long term time series and propose Pseudo-nitzschia allochrona, a new cryptic diatom, as a possible case of speciation by temporal segregation. The new species differs in several genetic markers (18S, LSU and ITS rDNA fragments and rbcL) and is reproductively isolated from its closest relative, which is morphologically identical. Data from a long term plankton time series show Pseudo-nitzschia allochrona invariably occurring in summer-autumn in the Gulf of Naples, where its sister species are instead found in winter-spring. Temperature and nutrients are the main factors associated with the occurrence of P. allochrona, which could have evolved in sympatry by switching its phenology and occupying a new ecological niche. This case of possible speciation by time shows the relevance of combining ecological time series with molecular information to shed light on the eco-evolutionary dynamics of marine microorganisms.

evolutionary biology↗

bioRxiv2021

A robust approach to estimate relative phytoplankton cell abundance from metagenomic data

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Phytoplankton communities are generally studied by PCR amplification of bacterial (16S), nuclear (18S) or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. In addition, rRNA marker genes fail to capture both cyanobacteria and photosynthetic eukaryotes simultaneously. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the Tara Oceans datasets, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these organisms, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.

ecology↗

bioRxiv2019

Higher prevalence of homologous recombination-deficiency in lung squamous carcinoma from African Americans

To improve our understanding of the longstanding disparities in incidence and mortality across multiple cancer types among minority populations, we performed a systematic comparative analysis of molecular features in tumors from African American (AA) and European American (EA) ancestry. Our pan-cancer analysis on the cancer genome atlas (TCGA) and a more focused analysis of genome-wide somatic copy number profiles integrated with tumor-normal RNA sequencing in a racially balanced cohort of 222 non-small cell lung cancers (NSCLC) reveals more aggressive genomic characteristics of AA tumors. In general, we find AA tumors exhibit higher genomic instability (GI), homologous recombination-deficiency (HRD) levels, and more aggressive molecular features such as chromothripsis across many cancer types, including lung squamous carcinoma (LUSC). GI and HRD levels are strongly correlated across AA tumors, indicating that HRD plays an important role in GI in these patients. The prevalence of germline HRD is higher in AA tumors, suggesting that the somatic differences observed have genetic ancestry origins. Finally, we identify AA-specific copy number-based arm, focal and gene level recurrent features in lung cancer, including a higher frequency of PTEN deletion and KRAS amplification and a lower frequency of CDKN2A deletion. These results highlight the importance of including minority and under-represented populations in genomics research and may have therapeutic implications.

cancer biology↗