Biology subjects

de Sousa, J. A.

Publications and source records attributed to de Sousa, J. A..

4 recordsLinked to original sources

bioRxiv2024

In vivo reprogramming of Caenorhabditis elegans leads to heterogeneous effects on lifespan

In the last decade, cellular reprogramming of fully differentiated cells to pluripotent stem cells has become of great interest. Importantly, cellular reprogramming by expression of Oct4, Sox2, Klf4, and cMyc (OSKM) can ameliorate age-associated phenotypes in multiple tissues and extend lifespan in progeroid and aged wild-type mice. Surprisingly, the effects of in vivo reprogramming have not been deeply investigated in any other model organisms. Here, for the first time, we induce in vivo reprogramming in C. elegans using a heat-inducible system at multiple developmental and adult stages. Similar to mice, expression of the reprogramming factors leads to premature death with different levels of toxicity at distinct developmental stages and aging. In vivo reprogramming in C. elegans might represent a valuable tool to improve our understanding of development and in vivo reprogramming.

cell biology↗

bioRxiv2024

Comparative analysis of mouse strains for in vivo reprogramming

In vivo reprogramming through the forced expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) has demonstrated great potential for reversing age-associated phenotypes, as the combination of these transcription factors actively promote cell regeneration and rejuvenation in various tissues and organs. However, continuous in vivo OSKM expression raised safety concerns due to loss of cell identity, decrease in body weight, and premature death. Although cyclic short-term or targeted expression of the reprogramming factors can mitigate some of these detrimental effects in mice, systemic rejuvenation of wild type mice has remained elusive potentially due to these current technical limitations. To improve the fundamental understanding of in vivo reprogramming, we conducted a comparative analysis across multiple reprogrammable mouse strains, tissues, and expression methods, presenting a comprehensive atlas of formerly established strains. In addition, we developed novel reprogrammable mouse strains by avoiding OSKM expression in specific organs, in dividing cells, or implementing chimeric expression approaches within specific cells, thereby offering safer strategies to induce in vivo reprogramming and fully harness its potential. We hope that these new tools will become valuable resources for future research in this very exciting field of research with potential implications to human health.

molecular biology↗

bioRxiv2022

Competition between phage-resistance mechanisms determines the outcome of bacterial co-existence

Many bacterial species carry multiple prophages. Despite their potential cost, these elements can provide multiple fitness advantages to the host, such as the elimination of direct competitors. However, the long-term efficiency of prophage induction to displace competitors has received little attention. We experimentally coevolved a polylysogenic Klebsiella pneumoniae strain (ST14) with a phage-sensitive strain (BJ1) in several environments resulting in different phage pressures. We then followed the adaptation process and the emergence of resistance. After 30 days, population yield remained stable, and although BJ1 was present in all conditions, its frequency was higher when phage pressure was stronger. Resistance to phages emerged quickly through mutations that prevent capsule biosynthesis. In contrast to our expectation, lysogenic conversion was rare and costly because new BJ1 lysogens exhibited exacerbated death rates and were easily outcompeted. Unexpectedly, the adaptation process changed at longer time scales, where BJ1 populations adapted by fine-tuning the production of capsule, reducing the ability of phage to absorb, while remaining capsulated. These resistant clones are pan-resistant to a large panel of phages. Most intriguingly, some clones exhibited transient non-genetic resistance to phages. Our experimental and modelling results highlight the diversity, dynamics and competition between phage-resistance mechanisms during coevolution and how these are driven by phage pressure.

evolutionary biology↗

bioRxiv2020

Bacteria have numerous phage-plasmid families with conserved phage and variable plasmid gene repertoires.

Plasmids and temperate phages are mobile genetic elements driving bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage-plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage-plasmids are poorly known. Here, we screened for these elements among ca. 14000 phages and plasmids and identified 780 phage-plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to define 8 families and 18 other broader communities of elements. The existence of these large groups suggests that phage-plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage-plasmids and found the key phage genes to be conserved and co-localized within families, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage-plasmids are a sizeable fraction of all phages and plasmids and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.

genomics↗