Biology subjects

Giordano, D.

Publications and source records attributed to Giordano, D..

5 recordsLinked to original sources

bioRxiv2024

The mitochondrial orf125 affects male fertility of Solanum tuberosum (+) S. commersonii somatic hybrids and participates in the onset of ''Tuberosum''-Type CMS and evolution of common potato

Cytoplasmic male sterility (CMS) is an agronomically significant trait and a powerful tool to study interactions between nuclear and cytoplasmic genomes. In this study, the chondriomes of two isonuclear male-fertile and sterile somatic hybrids (SH9A and SH9B, respectively) between the common potato (Solanum tuberosum Group Tuberosum, tbr) and the wild species S. commersonii (cmm), were sequenced and compared to those of parental species to identify mitochondrial genes involved in the expression of male sterility. A putative novel gene (orf125) was found only in tbr and in male-sterile hybrids. Two approaches, a physical or functional deletion of orf125 by mtDNA editing in SH9B and its allotopic expression in SH9A, clearly demonstrate that orf125 affects male fertility. To trace the origin of orf125 and hypothesize its role in the evolution of common potato, we searched it in tbr varieties, tuber-bearing potato relatives and other Solanaceae. The organization of the mitochondrial genome region implicated in CMS remained consistent across all common potato accessions in GenBank. An identical tbr copy of orf125 was also detected in all six accessions belonging to the S. berthaultii complex (ber) analyzed. Such findings corroborate the hypothesis that ber accessions with T/{beta} cytoplasm crossed as female with Andean potato (S. tuberosum Group Andigenum, adg), giving rise to the differentiation of the Chilean potato (S. tuberosum Group Chilotanum), and highlights the origin of mitochondrial factors contributing to genic-cytoplasmic male sterility in tbr x adg (or some wild species) hybrids.

plant biology↗

bioRxiv2022

In Silico Analysis Of The Effects Of Omicron Spike Amino Acid Changes On The Interactions With Human ACE2 Receptor And Structurally Characterized Complexes With Human Antibodies

The new SARS-CoV-2 variant Omicron is characterised, among others, by more than 30 amino acid changes (including 4 deletions and 1 insertion) occurring on the spike glycoprotein. We report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human ACE2 receptor or with human antibodies, obtained by analysing the publicly available resolved 3D structures. Our analysis predicts that amino acid changes occurring on amino acids interacting with the ACE2 receptor may increase Omicron transmissibility. The interactions of Omicron spike with human antibodies can be both negatively and positively affected by amino acid changes, with a predicted total loss of interactions only in few complexes. We believe that such an approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology, especially when extended to other than spike proteins.

bioinformatics↗

bioRxiv2021

On the capacity of putative plant odorant-binding proteins to bind volatile plant isoprenoids

Plants use odors not only to recruit other organisms for symbioses, but to talk to each other. Volatile organic compounds (VOCs) from "emitting" plants inform the "receiving" (listening) plants of impending stresses or simply of their presence. However, the receptors that allow receivers to perceive the volatile cue are elusive. Most likely, plants (as animals) have odorant bind proteins (OBPs), and in fact few OBPs are known to bind "stress-induced" plant VOCs. We investigated whether OBPs may bind volatile constitutive and stress-induced isoprenoids, the most emitted plant VOCs, with well-established roles in plant communication. First, we performed a data base search that generated a list of candidate plant OBPs. Second, we investigated in silico the ability of the identified candidate plant OBPs to bind VOCs by molecular simulation experiments. Our results show that monoterpenes can bind the same OBPs that were described to bind other stress-induced VOCs. Whereas, the constitutive hemiterpene isoprene does not bind any investigated OBP and may not have an info-chemical role. We conclude that, as for animal, plant OBPs may bind different VOCs. Despite being generalist and not specialized, plant OBPs may play an important role in allowing plants to eavesdrop messages sent by neighboring plants.

plant biology↗

bioRxiv2020

Correct block-design experiments mitigate temporal correlation bias in EEG classification

It is argued in [1] that [2] was able to classify EEG responses to visual stimuli solely because of the temporal correlation that exists in all EEG data and the use of a block design. While one of the analyses in [1] is correct, i.e., that low-frequency slow EEG activity can inflate classifier performance in block-designed studies [2], as we already discussed in [3], we here show that the main claim in [1] is drastically overstated and their other analyses are seriously flawed by wrong methodological choices. Our counter-analyses clearly demonstrate that the data in [2] show small temporal correlation and that such a correlation minimally contributes to classification accuracy. Thus, [1]s analysis and criticism of block-design studies does not generalize to our case or, possibly, to other cases. To validate our counter-claims, we evaluate the performance of several state-of-the-art classification methods on the dataset in [2] (after properly filtering the data) reaching about 50% classification accuracy over 40 classes, lower than in [2], but still significant. We then investigate the influence of EEG temporal correlation on classification accuracy by testing the same models in two additional experimental settings: one that replicates [1]s rapid-design experiment, and another one that examines the data between blocks while subjects are shown a blank screen. In both cases, classification accuracy is at or near chance, in contrast to what [1] reports, indicating a negligible contribution of temporal correlation to classification accuracy. We, instead, are able to replicate the results in [1] only when intentionally contaminating our data by inducing a temporal correlation. This suggests that what Li et al. [1] demonstrate is simply that their data are strongly contaminated by temporal correlation and low signal-to-noise ratio. We argue that the reason why Li et al. in [1] observe such high correlation in EEG data is their unconventional experimental design and settings that violate the basic cognitive neuroscience study design recommendations, first and foremost the one of limiting the experiments duration, as instead done in [2]. The reduced stimulus-driven neural activity, the removal of breaks and the prolonged duration of experiments in [1], removed the very neural responses that one would hope to classify, leaving only the amplified slow EEG activity consistent with a temporal correlation. Furthermore, the influence of temporal correlation on classification performance in [1] is exacerbated by their choice to perform per-subject classification rather than the more commonly-used and appropriate pooled subject classification as in [2]. Our analyses and reasoning in this paper refute the claims of the "perils and pitfalls of block-design" in [1]. Finally, we conclude the paper by examining a number of other oversimplistic statements, inconsistencies, misinterpretation of machine learning concepts, speculations and misleading claims in [1]. NoteThis paper was prepared as a response to [1] before its publication and we were not given access to the code (although its authors had agreed, through the PAMI EiC, to share it with us). For this reason, in the experiments presented in this work we employed our own implementation of their model.

bioengineering↗

bioRxiv2020

Extending rnaSPAdes functionality for hybridtranscriptome assembly

BackgroundDe novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. ResultsIn this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. ConclusionTo evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used. Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available for Linux and MacOS under GPLv2 license at cab.spbu.ru/software/rnaspades/ and github.com/ablab/spades.

bioinformatics↗