Search

Background: Physical activity (PA) can play a role in lowering the risk of breast cancer (BC), but also in reducing perioperative complications and treatments related side effects, improving the quality of life and decreasing mortality in BC survivors. PA and nutritional screening are not offered to patients after cancer diagnosis as standard of care, even in high quality breast units. Methods: From February 2019 to March 2020, we performed a preoperative physical and nutritional screening in 504 consecutive BC patients waiting for surgery. The screening included an IPAQ questionnaire to evaluate the level of physical activity; nutritional screening with measurement of anthropometric parameters (weight, height, waist and hips circumference, BMI, and waist hip ratio) and evaluation of body composition using Bioelectrical Impedance Analysis (BIA). Results: The majority of patients in our series resulted physically inactive: clustering the IPAQ scores, 47% of patients proved to be physically inactive (MET score <700), 34% moderately active (MET score 700-2520), and only 19% physically active (MET score > 2520). In addition, approximately half of the patients (49.01%) resulted overweight or obese, and more than half (55.2%) had a percentage of fatty tissue over the recommended cut off for adult women. Conclusions: Our data confirm that assessment of PA levels should become part of the standard preoperative evaluation of BC patients and behavioral interventions should be offered to them, in order to pre-habilitate for surgery and improve outcomes. IPAQ Questionnaire and body composition analysis could be quick and easy screening tools in order to identify which patients may need more support in being active during and after anticancer treatments. [ABSTRACT FROM AUTHOR]

This paper is part of a wider study about a corpus of songs, collected in the three different languages spoken in Salento (Puglia- South Italy): Italian (with regional variety), Griko and Salentino dialect. We analyze all the discography (texts and music of songs) of Avleddha , one of the most famous popular bands, founded in the early '90s in the Grecìa Salentina. This corpus is compared to other 80 songs, that includes English, Italian and popular music. We use Principal Component Analysis and techniques of sound analysis (spectrograms) we demonstrate that songs of the four bands are well separated from a point of view of complexity of the texts and music. The aim of this study is to characterize Avleddha's music with reference to the other group of songs. We show that it is closer to the tradition of Salento popular music, but is able to maintain an original fingerprint, that makes it unique in its field. In this research the description of language systems at morphosyntactic level is not present, but we present a novel quantitative approach to reveal features both generic and specific in corpora of popular music. [ABSTRACT FROM AUTHOR]

Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias. Confirming previous results on E. coli , we show the existence of a universal exponential relation between gene essentiality and conservation in bacteria. Moreover, we show that, within each bacterial genome, there are at least two groups of functionally distinct genes, characterised by different levels of conservation and codon bias: i) a core of essential genes, mainly related to cellular information processing; ii) a set of less conserved nonessential genes with prevalent functions related to metabolism. In particular, the genes in the first group are more retained among species, are subject to a stronger purifying conservative selection and display a more limited repertoire of synonymous codons. The core of essential genes is close to the minimal bacterial genome, which is in the focus of recent studies in synthetic biology, though we confirm that orthologs of genes that are essential in one species are not necessarily essential in other species. We also list a set of highly shared genes which, reasonably, could constitute a reservoir of targets for new anti-microbial drugs. [ABSTRACT FROM AUTHOR]

Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for E.coli, comparing CompAI with other widely used indices: tAI, CAI, and Nc. We show that CompAI and tAI capture similar information by being positively correlated with gene conservation, measured by the Evolutionary Retention Index (ERI), and essentiality, whereas, CAI and Nc appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of tAI and CompAI with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in E.coli. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by CompAI and tAI). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, CompAI turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation. Notably, CompAI may potentially correlate with translation speed measurements, by accounting for the specific delay induced by wobble-pairing between codons and anticodons. [ABSTRACT FROM AUTHOR]

We study the correlation between the codon usage bias of genetic sequences and the network features of protein-protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with similar patterns of codon usage have a significantly higher probability that their encoded proteins are functionally connected and interacting. Importantly, this signal emerges when multiple aspects of codon bias are taken into account at the same time. The present study extends our previous observations on E. coli over a wide set of 34 bacteria. These findings could allow for future investigations on the possible effects of codon bias on the topology of the PPI network, with the aim of improving existing bioinformatics methods for predicting protein interactions. [ABSTRACT FROM AUTHOR]

The relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which first occurred in Wuhan (China) in December of 2019, causes a severe acute respiratory illness with a high mortality rate, and has spread around the world. To gain an understanding of the evolution of the newly emerging SARS-CoV-2, we herein analyzed the codon usage pattern of SARS-CoV-2. For this purpose, we compared the codon usage of SARS-CoV-2 with that of other viruses belonging to the subfamily of Orthocoronavirinae. We found that SARS-CoV-2 has a high AU content that strongly influences its codon usage, which appears to be better adapted to the human host. We also studied the evolutionary pressures that influence the codon usage of five conserved coronavirus genes encoding the viral replicase, spike, envelope, membrane and nucleocapsid proteins. We found different patterns of both mutational bias and natural selection that affect the codon usage of these genes. Moreover, we show here that the two integral membrane proteins (matrix and envelope) tend to evolve slowly by accumulating nucleotide mutations on their corresponding genes. Conversely, genes encoding nucleocapsid (N), viral replicase and spike proteins (S), although they are regarded as are important targets for the development of vaccines and antiviral drugs, tend to evolve faster in comparison to the two genes mentioned above. Overall, our results suggest that the higher divergence observed for the latter three genes could represent a significant barrier in the development of antiviral therapeutics against SARS-CoV-2. [ABSTRACT FROM AUTHOR]

We discuss a phase transition in spin glass models that have been rarely considered in the past, namely, the phase transition that may take place when two real replicas are forced to be at a larger distance (i.e., at a smaller overlap) than the typical one. In the first part of the work, by solving analytically the Sherrington-Kirkpatrick model in a field close to its critical point, we show that, even in a paramagnetic phase, the forcing of two real replicas to an overlap small enough leads the model to a phase transition where the symmetry between replicas is spontaneously broken. More importantly, this phase transition is related to the de Almeida-Thouless (dAT) critical line. In the second part of the work, we exploit the phase transition in the overlap between two real replicas to identify the critical line in a field in finite dimensional spin glasses. This is a notoriously difficult computational problem, because of considerable finite size corrections. We introduce a new method of analysis of Monte Carlo data for disordered systems, where the overlap between two real replicas is used as a conditioning variate. We apply this analysis to equilibrium measurements collected in the paramagnetic phase in a field, h > 0 and T c (h) < T < T c (h = 0) , of the d = 1 spin glass model with long range interactions decaying fast enough to be outside the regime of validity of the mean field theory. We thus provide very reliable estimates for the thermodynamic critical temperature in a field. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first occurred in Wuhan (China) in December of 2019. Since the outbreak, it has accumulated mutations on its coding sequences to optimize its adaptation to the human host. The identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe., Methods: In this study, we compared 320,338 SARS-CoV-2 genomes isolated from all over the world to the first sequenced genome in Wuhan, China. To this end, we analysed over time the codon usage patterns of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp) and ORF1ab., Results: We found that genes coding for the proteins N and S diverged more rapidly since the outbreak by accumulating mutations. Interestingly, all genes show a deoptimization of their codon usage with respect to the human host. Our findings suggest a general evolutionary trend of SARS-CoV-2, which evolves towards a sub-optimal codon usage bias to favour the host survival and its spread. Furthermore, we found that S protein and RdRp are more subject to an increasing purifying pressure over time, which implies that these proteins will reach a lower tendency to accept mutations. In contrast, proteins N and M tend to evolve more under the action of mutational bias, thus exploring a large region of their sequence space., Conclusions: Overall, our study shed more light on the evolution of SARS-CoV-2 genes and their adaptation to humans, helping to foresee their mutation patterns and the emergence of new variants., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s). Published by IMR Press.)

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that first occurred in Wuhan in December 2019. The spike glycoproteins and nucleocapsid proteins are the most common targets for the development of vaccines and antiviral drugs., Objective: We herein analyze the rate of evolution along with the sequences of spike and nucleocapsid proteins in relation to the spatial locations of their epitopes, previously suggested to contribute to the immune response caused by SARS-CoV-2 infections., Methods: We compare homologous proteins of seven human coronaviruses: HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HCoV-HKU1, MERS-CoV, and SARS-CoV-2. We then focus on the local, structural order-disorder propensity of the protein regions where the SARS-CoV-2 epitopes are located., Results: We show that most of nucleocapsid protein epitopes overlap the RNA-binding and dimerization domains, and some of them are characterized by a low rate of evolutions. Similarly, spike protein epitopes are preferentially located in regions that are predicted to be ordered and well- conserved, in correspondence of the heptad repeats 1 and 2. Interestingly, both the receptor-binding motif to ACE2 and the fusion peptide of spike protein are characterized by a high rate of evolution., Conclusion: Our results provide evidence for conserved epitopes that might help develop broad-spectrum SARS-CoV-2 vaccines., (© 2021 Bentham Science Publishers.)

Background: Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work, we relate conservation, essentiality and functional repertoire of a gene to the connectivity k ( i.e. the number of interactions, links) of the corresponding protein in the PPI network., Methods: On a set of 42 bacterial genomes of different sizes, and with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivities changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolutionary retention index (ERI) and by evolutionary pressures, is related to the connectivity of the corresponding protein; iii) how PPI connectivities are modulated by evolutionary and functional relationships, as represented by the Clusters of Orthologous Genes (COGs)., Results: We show that conservation, essentiality and functional specialisation of genes constrain the connectivity of the corresponding proteins in bacterial PPI networks. In particular, we isolated a core of highly connected proteins (connectivities k≥ 40), which is ubiquitous among the species considered here, though mostly visible in the degree distributions of bacteria with small genomes (less than 1000 genes)., Conclusion: The genes that support this highly connected core are conserved, essential and, in most cases, belong to the COG cluster J, related to ribosomal functions and the processing of genetic information., (© 2021 Bentham Science Publishers.)