Biology subjects

Ortiz, E.

Publications and source records attributed to Ortiz, E..

6 recordsLinked to original sources

bioRxiv2026

The interaction of dispersal, species sorting, and priority effects, explains a unimodal response of β-diversity to immigration rates

A dominant perspective in metacommunity theory is that dispersal consistently homogenizes species composition across local communities. However, recent studies have reported a direct relationship between dispersal rate and {beta}-diversity, which has been attributed to the influence of priority effects and species sorting. The underlying mechanisms by which dispersal can either increase or decrease {beta}-diversity remain unclear, hindering our understanding of metacommunity assembly and the processes driving biodiversity patterns across time and space. We theoretically evaluated how purely random priority effects, priority effects conditioned by species dispersal abilities, and species sorting shape the {beta}-diversity-dispersal relationship in metacommunities open to exogenous dispersal (i.e., immigration) from a regional species pool. Our results show that the three evaluated processes foster community differentiation at intermediate exogenous dispersal rates when dispersal between communities (i.e. endogenous dispersal) is taking place. Additionally, the interaction between endogenous and exogenous dispersal homogenizes communities at low and high exogenous dispersal rates, determining a unimodal response of {beta}-diversity to increasing exogenous dispersal rates. Our findings contribute to a deeper mechanistic understanding of metacommunity assembly and offer a coherent explanation for previously observed empirical discrepancies, thereby challenging the traditional view of dispersal as a purely homogenizing process.

ecology↗

bioRxiv2025

Hetero-multicellular stromal cells incorporate into scaffold-free 3D cultures of epithelial cancer cells to drive invasion

Breast cancer (BC) is the second leading cause of cancer-related death among women in the U.S. Organoid models of solid tumors have been shown to faithfully recapitulate aspects of cancer progression such as proliferation and invasion. Although patient-derived organoids (PDOs) and patient-derived xenograft organoids (PDXOs) are pathophysiologically relevant, they are costly to propagate, difficult to manipulate and comprised primarily of the most proliferative cell types within the tumor microenvironment (TME). These limitations prevent their use for elucidating cellular mechanisms of disease progression that depend upon tumor-associated stromal cells which are found within the TME and known to contribute to metastasis and therapy resistance. Here, we report on methods for cultivating epithelial-stromal multicellular 3D cultures. Advantages of these methods include a cost-effective system for rapidly generating organoid-like 3D cultures within scaffold-free environments that can be used to track invasion at single-cell resolution within hydrogel scaffolds. Specifically, we demonstrate how to generate these hetero-multicellular 3D cultures using BT-474 breast cancer cells in combination with fibroblasts (BJ-5ta), monocyte-like cells(THP-1) and/or endothelial cells (EA.hy926). Additionally, differential fluorescent labeling of cell populations enables time-lapse microscopy to define 3D culture assembly and invasion dynamics. Notably, the addition of any two stromal cell combinations to 3D cultures of BT-474 cells significantly reduces circularity of the 3D cultures, consistent of the presence of organoid-like or secondary spheroid structures. In tracker dye experiments, fibroblasts and endothelial cells co-localize in the peripheral organoid-like protrusions and are spatially segregated from the primary BT-474 spheroid. Finally, hetero-multicellular 3D cultures of BT-474 cells have increased hydrogel invasion capacity. Since we observed these protrusive structures in hetero-multicellular 3D cultures of both non-tumorigenic and tumorigenic breast epithelial cells, this work provides an efficient and reproducible method for generating organoid-like 3D cultures in a scaffold-free environment for subsequent analyses of phenotypes associated with solid tumor progression. SUMMARYThere is a critical need for 3D cancer models that capture hetero-cellular crosstalk to study cancer metastasis. Our study presents the generation of hetero-multicellular stromal-epithelial in a scaffold and scaffold free environment that can be used to study invasion and cellular spatial distributions.

cancer biology↗

bioRxiv2022

Visual Perception of 3D Space and Shape In Time - Part IV: 3D Shape Recognition by 3D Rotation

Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear at any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size upfront at the object center, the direct comparison between the one-sized memory and an incoming new image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly as we experience it in our daily lives? This paper specifically addresses the recognition of human faces with arbitrary 3D orientation in the [Roll, Yaw, Pitch] axes. According to our new model of NHT (Neural Holography Tomography), space is represented by time utilizing the phase of the alpha brainwave. This principle should be applicable to any mental rotation in 3D; thus, it predicts that extra time is required to perceive a rotated face to revolve it back to upright by the constant-speed alpha wave. To assess this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of upright unfamiliar faces. Following the memorization phase, similar stimuli with a wide range of rotating faces in 3D were presented, and RTs were recorded. As expected, the memorized upfront face was the fastest RT. The excess of the RT was observed proportional to the rotating angle in all [Roll, Yaw, Pitch] axes. Roll had the flattest slope, whereas upper Pitch was the steepest. We suspect that Roll is the swiftest mental operation because it can be conducted by the linear frame translation on the log-polar retinotopy of the visual cortex.

neuroscience↗

bioRxiv2021

Central nervous system hypomyelination disrupts axonal conduction and behaviour in larval zebrafish

Myelination is essential for central nervous system (CNS) formation, health and function. As a model organism, larval zebrafish have been extensively employed to investigate the molecular and cellular basis of CNS myelination, due to their genetic tractability and suitability for non-invasive live cell imaging. However, it has not been assessed to what extent CNS myelination affects neural circuit function in zebrafish larvae, prohibiting the integration of molecular and cellular analyses of myelination with concomitant network maturation. To test whether larval zebrafish might serve as a suitable platform with which to study the effects of CNS myelination and its dysregulation on circuit function, we generated zebrafish myelin regulatory factor (myrf) mutants with CNS-specific hypomyelination and investigated how this affected their axonal conduction properties and behaviour. We found that myrf mutant larvae exhibited increased latency to perform startle responses following defined acoustic stimuli. Furthermore, we found that hypomyelinated animals often selected an impaired response to acoustic stimuli, exhibiting a bias towards reorientation behaviour instead of the stimulus-appropriate startle response. To begin to study how myelination affected the underlying circuitry, we established electrophysiological protocols to assess various conduction properties along single axons. We found that the hypomyelinated myrf mutants exhibited reduced action potential conduction velocity and an impaired ability to sustain high frequency action potential firing. This study indicates that larval zebrafish can be used to bridge molecular and cellular investigation of CNS myelination with multiscale assessment of neural circuit function.

neuroscience↗

bioRxiv2020

Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages

Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages-Powerpuff, Lego, and YesChef-which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ and Microbacterium Cluster EH, as well as the former Microbacterium singleton Zeta1847, exhibited low nucleotide similarity but gene content similarity in excess of the recently adopted Microbacterium clustering parameter, which resulted in the reassignment of Zeta1847 to Cluster EH. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle; in the first experimental verification of a Cluster AZ phages life cycle, we show that phage Powerpuff is a true temperate phage and forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages encoding an integrase but lacking an identified repressor may be temperate as well. Our findings further highlight the importance of using multiple metrics to capture phage relatedness, provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera, and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.

microbiology↗

bioRxiv2018

Effects of shade-coffee certification programs on bird, trees and butterfly diversity in Colombia

In the last decade coffee certification programs have grown rapidly in Latin America, encouraging producers to harvest coffee based on production standards intended to enhance biodiversity conservation. However, few studies have tested whether such programs have a positive conservation impact. To date, research has focused on comparing community similarity between forests and plantations, but the question of whether certified plantations provide refuges for biodiversity in regions where all the forest has been lost remains untested. Here, we compare bird, butterfly and plant communities in highly deforested regions in Santander, Colombia, to determine the potential conservation role of two certification programs: Rainforest Alliance and Rainforest Alliance+Organic. We used 13 farms to census birds, butterflies, and trees, and quantified structural characteristics of the shade. We found little difference in most measures of diversity and composition of birds, butterfly and plant communities between types of plantations. However, despite high variation across farms, butterfly richness and abundance increased with the decrease in the use of pesticides in plantations. These results suggest that reduced use of chemical compounds in certified coffee plantations might enhance conservation of butterfly communities. The biodiversity associated with these coffee plantations and the high deforestation rates in Santander, suggest that irrespective of their certification type they provide the last refuges for biodiversity conservation in this region.

ecology↗