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Lozano, A.

Publications and source records attributed to Lozano, A..

20 records · Page 2Linked to original sources

Preparation of DPPC liposomes using probe-tip sonication: investigating intrinsic factors affecting temperature phase transitions

Liposomes are an important tool and have gained much attention for their promise as an effective means of delivering small therapeutic compounds to targeted sites. In an effort to establish an effective method to produce liposomes from the lipid, dipalmitoyl-phosphatidylcholine or DPPC, we have found important aspects that must be taken into consideration. Here, we used probe-tip sonication to prepare liposomes on a batch scale. During this process we uncovered interesting steps in their preparation that altered the thermodynamic properties and phase transitions of the resulting liposome mixtures. Using differential scanning calorimetry to assess this we found that increasing the sonication time had the most dramatic effect on our sample, producing almost an entirely separate phase transition relative to the main phase transition. This result is consistent with reports from the current literature. We also highlight a smaller transition, which we attribute to traces of unincorporated lipid that seems to gradually disappear as the total lipid concentration decreases. Overall, sonication is an effective means of producing liposomes, but we cannot assert this method is optimal in producing them with precise physical properties. Here we highlight the physical effects at play during this process.

biophysics↗

Robust Estimation Of Hi-C Contact Matrices Using Fused Lasso Reveals Preferential Insulation Of Super-Enhancers By Strong TAD Boundaries

The metazoan genome is compartmentalized in megabase-scale areas of highly interacting chromatin known as topologically associating domains (TADs), typically identified by computational analyses of Hi-C sequencing data. TADs are demarcated by boundaries that are largely conserved across cell types and even across species, although, increasing evidence suggests that the seemingly invariant TAD boundaries may exhibit plasticity and their insulating strength can vary. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. A systematic classification and characterization of TAD boundaries may generate new insights into their function. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score. We demonstrate that higher TAD boundary insulation scores are associated with elevated CTCF levels and that they may differ across cell types. Intriguingly, we observe that super-enhancer elements are preferentially insulated by strong boundaries, i.e. boundaries of higher insulation score. Furthermore, we perform a pan-cancer analysis to demonstrate that strong TAD boundaries and super-enhancer elements are frequently co-duplicated in cancer patients. Taken together, our findings suggest that super-enhancers insulated by strong TAD boundaries may be exploited, as a functional unit, by cancer cells to promote oncogenesis.

bioinformatics↗