Biology subjects

Aleman, J. A.

Publications and source records attributed to Aleman, J. A..

3 recordsLinked to original sources

bioRxiv2023

Electrophoresis-Based Approach for Characterizing Dendrimer-Protein Interactions: A Proof-of-Concept Study

Improving the clinical translation of nanomedicine requires better knowledge about how nanoparticles interact with biological environments. As researchers are recognizing the importance of understanding the protein corona and characterizing how nanocarriers respond in biological systems, new tools and techniques are needed to analyze nanocarrier-protein interactions, especially for smaller-size (<10nm) nanoparticles like polyamidoamine (PAMAM) dendrimers. Here we developed a streamlined, semi-quantitative approach to assess dendrimer-protein interactions using a non-denaturing electrophoresis technique combined with mass spectrometry. With this protocol, we detect fluorescently tagged dendrimers and proteins simultaneously, enabling us to analyze when dendrimers migrate with proteins. We found PAMAM dendrimers mostly interact with complement proteins, particularly C3 and C4a, which aligns with previously published data, verifying our approach can be used to isolate and identify dendrimer-protein interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/555747v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@102bdeeorg.highwire.dtl.DTLVardef@103914corg.highwire.dtl.DTLVardef@138402eorg.highwire.dtl.DTLVardef@1fdbbd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Divergent lineages in a young species: the case of Datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula

PremiseGlobally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula, in western North America, exhibit strong genetic structure and highly concordant divergent lineages across their ranges, as they were isolated during the Pleistocene glacial-interglacial cycles and thus accumulated genetic differentiation in their genomes. A representative plant genus of this Peninsula is Yucca, with Yucca valida having the widest range. Whereas Y. valida is a dominant species, there is an extensive distribution discontinuity between 26{degrees} N and 27{degrees} N, where no individuals have been identified, suggesting restricted gene flow. Moreover, the historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. MethodsWe examined the phylogeography of Y. valida throughout its range to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the species age. Key resultsWe assembled 4,411 SNPs from 147 plants, identifying three allopatric lineages. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age under one million years for the common ancestor of Y. valida and its sister species. ConclusionsHabitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.

evolutionary biology↗

bioRxiv2023

Development of genomic resources for cattails (Typha), a globally important macrophyte genus

1. BackgroundA critical knowledge gap in freshwater plants research is the lack of genetic tools necessary to answer fundamental questions about their demographic histories, adaptation, and phylogenetic relationships. One example of this is Typha, a global genus of freshwater plants foundational to wetlands that is also becoming an increasingly problematic biological invader in numerous regions worldwide; while important insights have been discovered for this genus, existing markers are insufficient to answer fundamental questions about their demographic histories, adaptation, and phylogenetic relationships, to identify introduced and hybrid lineages, and to examine patterns of hybridisation and introgression. 2. MethodsWe optimised a library preparation and data processing protocol to develop genome-wide nuclear and plastid resources for studying the evolutionary history, genetic structure and diversity, hybridisation, local adaptation, invasiveness, and geographic expansion dynamics of Typha. 3. Main resultsWe sequenced 140 Typha samples and identified [~]120K nuclear SNPs that differentiate T. angustifolia, T. domingensis and T. latifolia and retrieved their plastome sequences. We observed genetic introgression among the three species. 4. ConclusionsFollowing a fast, straightforward, and cost-efficient genomic library preparation protocol, we produced a suite of genome-wide resources to facilitate investigations into the taxonomy and population genetics of Typha and to advance the genomic understanding of wetland plants. 5. ContributionsThe protocol described, the updated chromosome-level genome assembly of T. latifolia, the catalogue of species-specific SNPs, and the chloroplast sequences produced in this study comprise permanent resources that can be applied to study the genetic composition of multiple populations and hybrid zones and will be incorporated into future studies of Typha, an ecologically important and globally invasive macrophyte.

molecular biology↗