Biology subjects

Castano, N.

Publications and source records attributed to Castano, N..

4 recordsLinked to original sources

bioRxiv2023

New variants in the Chloroplast Genome Sequence of two Colombian individuals of the Cedar timber species (Cedrela odorata L.), using long read Oxford Nanopore Technology

The plant species Cedrela odorata has been largely exploited in the timber industry due to the high demand of its wood. Therefore, C. odorata, has been considered as a vulnerable species since 1994, with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). C. odorata is one of the key timber species included in the management and conservation plans in Colombia. These plans include the study of local populations by developing genetic resources for the species. In this study, two novel chloroplast (cp) genomes have been generated using the MinION long read sequencing technology. The new cp assemblies were compared with other cp genomes for the species, supporting previous hypothesis of intraspecific diversity associated to their place of origin. Furthermore, the cp genomes were screened for sequence variants (SV) and a total of 16 SNPs were identified, presumably unique to populations of the amazon region in Colombia. Here, the first cp genome sequences of C. odorata from Colombian individuals represent novel and valuable genomic resources for the species suitable for DNA fingerprinting and DNA barcoding applications.

plant biology↗

bioRxiv2023

Major axes of variation in tree demography across global forests

The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatial-temporal patterns in tree population dynamics. While historical research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach is to group mechanisms according to their shared effects on the variability of tree vital rates and to quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions, categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6,500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28-33% of demographic variance alone, and in interaction with space 14-17%, totalling 40-43%. The average variability among species declined with species richness across forests, indicating that diverse forests featured smaller interspecific differences in vital rates supporting the theory that the range of vital rates is similar across global forests. Decomposing the variance in vital rates into the proposed OPs showed that taxonomy is crucial to predicting and understanding tree demography on large forest plots. A focus on how variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.

ecology↗

bioRxiv2022

Hydrodynamic dissection of single cells in a microfluidic system

Stentor coeruleus, a single-cell ciliated protozoan, is a model organism for wound healing and regeneration studies. Despite Stentors large size (up to 2 mm in extended state), microdissection of Stentor remains challenging. In this work, we describe a hydrodynamic cell splitter, consisting of a cross junction, capable of splitting Stentor cells in a non-contact manner at a high throughput of [~]500 cells/min under continuous operation. Introduction of asymmetry in the flow field at the cross junction leads to asymmetric splitting of the cells to generate cell fragments as small as [~]8.5 times the original cell size. Characterization of cell fragment viability shows reduced 5-day survival as fragment size decreases and as the extent of hydrodynamic stress imposed on the fragments increases. Our results suggest that cell fragment size and composition, as well as mechanical stress, play important roles in the long-term repair of Stentor cells and warrant further investigations. Nevertheless, the hydrodynamic splitter can be useful for studying phenomena immediately after cell splitting, such as the closure of wounds in the plasma membrane which occurs on the order of 100 - 1000 seconds in Stentor.

biophysics↗

bioRxiv2022

Exponential magnetophoretic gradient for the direct isolation of basophils from whole blood in a microfluidic system

Despite their rarity in peripheral blood, basophils play important roles in allergic disorders and other diseases including sepsis and COVID-19. Existing basophil isolation methods require many manual steps and suffer from significant variability in purity and recovery. We report an integrated basophil isolation device (i-BID) in microfluidics for negative immunomagnetic selection of basophils directly from 100 L of whole blood within 10 minutes. We use a simulation-driven pipeline to design a magnetic separation module to apply an exponentially increasing magnetic force to capture magnetically tagged non-basophils flowing through a microtubing sandwiched between magnetic flux concentrators sweeping across a Halbach array. The exponential profile captures non-basophils effectively while preventing their excessive initial buildup causing clogging. The i-BID isolates basophils with a mean purity of 93.9%{+/-}3.6% and recovery of 95.6%{+/-}3.4% without causing basophil degradation or unintentional activation. Our i-BID has the potential to enable basophil-based point-of-care diagnostics such as rapid allergy assessment.

immunology↗