Biology subjects

Alvarez, M. M.

Publications and source records attributed to Alvarez, M. M..

7 recordsLinked to original sources

bioRxiv2022

The power of geohistorical boundaries for modeling the genetic background of human populations: the case of the rural Catalan Pyrenees

The genetic variation of the European population at a macro-geographic scale follows genetic gradients which reflect main migration events. However, less is known about factors affecting mating choices at a micro-geographic scale. In this study we have analyzed 726,718 autosomal SNPs in 435 individuals from the Catalan Pyrenees covering around 200 km of a vast and abrupt region in the north of the Iberian Peninsula, for which we have information about the geographic origin of all grand-parents and parents. At a macro-geographic scale, our analyses recapitulate the genetic gradient observed in Spain. However, we also identified the presence of micro-population substructure among the sampled individuals. Such micro-population substructure does not correlate with geographic barriers such as the expected by the orography of the considered region, but by the bishoprics present in the covered geographic area. These results support that, on top of main human migrations, long ongoing socio-cultural factors have also shaped the genetic diversity observed at rural populations.

genetics↗

bioRxiv2021

Use of standard U-bottom and V-bottom well plates to generate neuroepithelial embryoid bodies

The use of organoids has become increasingly popular recently due to their self-organizing abilities, which facilitate developmental and disease modeling. Various methods have been described to create embryoid bodies (EBs) generated from embryonic or pluripotent stem cells but with varying levels of differentiation success and producing organoids of variable size. Commercial ultra-low attachment (ULA) V-bottom well plates are frequently used to generate EBs. These plates are relatively expensive and not as widely available as standard concave well plates. Here, we describe a cost-effective and low labor-intensive method that creates homogeneous EBs at high yield in standard V- and U-bottom well plates by applying an antiadherence solution to reduce surface attachment, followed by centrifugation to enhance cellular aggregation. We also explore the effect of different seeding densities, in the range of 1 to 11 x103 cells per well, for the fabrication of neuroepithelial EBs. Our results show that the use of V-bottom well plates briefly treated with anti-adherent solution (for 5 min at room temperature) consistently yields functional neural EBs in the range of seeding densities from 5 to 11x103 cells per well. A brief post-seeding centrifugation step further enhances EB establishment. EBs fabricated using centrifugation exhibited lower variability in their final size than their noncentrifuged counterparts, and centrifugation also improved EB yield. The span of conditions for reliable EB production is narrower in U-bottom wells than in V-bottom wells (i.e., seeding densities between 7x103 and 11x103 and using a centrifugation step). We show that EBs generated by the protocols introduced here successfully developed into neural organoids and expressed the relevant markers associated with their lineages. We anticipate that the cost-effective and easily implemented protocols presented here will greatly facilitate the generation of EBs, thereby further democratizing the worldwide ability to conduct organoid-based research.

developmental biology↗

bioRxiv2021

Loss of HMCES is synthetic lethal with APOBEC activity in cancer cells

Analysis of cancer mutagenic signatures provides information about the origin of mutations and can inform the use of clinical therapies, including immunotherapy. In particular, APOBEC3A (A3A) has emerged as a major driver of mutagenesis in cancer cells and its expression results in DNA damage and susceptibility to treatment with inhibitors of the ATR and CHK1 checkpoint kinases. Here we report the implementation of CRISPR/Cas9 genetic screening to identify susceptibilities of multiple A3A-expressing lung adenocarcinoma cell lines. We identify HMCES, a protein recently linked to the protection of abasic sites, as a central protein for the tolerance of A3A expression. HMCES depletion results in synthetic lethality with A3A expression specifically in a TP53-mutant background. Analysis of previous screening data reveals a strong association between A3A mutational signatures and sensitivity to HMCES loss and indicates that HMCES is specialized in protecting against a narrow spectrum of DNA damaging agents in addition to A3A. We experimentally show that both HMCES disruption and A3A expression increase susceptibility of cancer cells to ionizing radiation, oxidative stress and ATR inhibition; strategies that are often applied in tumor therapies. Overall, our results suggest that HMCES is an attractive target for selective treatment of A3A expressing tumors.

cancer biology↗

bioRxiv2020

Biofabrication using maize protein: 3D printing using zein formulations

The use of three-dimensional (3D) printing for biomedical applications has expanded exponentially in recent years. However, the current portfolio of 3D printable inks is still limited. For instance, only a few protein matrices have been explored as printing/bioprinting materials. Here, we introduce the use of zein, the primary constitutive protein in maize seeds, as a 3D-printable material. Zein-based inks were prepared by dissolving commercial zein powder in ethanol with or without polyethylene glycol (PEG400) as a plasticizer. The rheological characteristics of our materials, studied during 21 days of aging/maturation, showed an increase in the apparent viscosity as a function of time in all formulations. The addition of PEG 400 decreased the apparent viscosity. Inks with and without PEG400 and at different maturation times were tested for printability in a BioX bioprinter. We optimized the 3D printing parameters for each ink formulation in terms of extrusion pressure and linear printing velocity. Higher fidelity structures were obtained with inks that had maturation times of 10 to 14 days. We present different proof-of-concept experiments to demonstrate the versatility of the engineered zein inks for diverse biomedical applications. These include printing of complex and/or free-standing 3D structures, materials for controlled drug release, and scaffolds for cell culture.

bioengineering↗

bioRxiv2020

Biofabrication of muscle fibers enhanced with plant viral nanoparticles using surface chaotic flows

Multiple human tissues exhibit fibrous nature. Therefore, the fabrication of hydrogel filaments for tissue engineering is a trending topic. Current tissue models are made of materials that often require further enhancement for appropriate cell attachment, proliferation and differentiation. Here we present a simple strategy, based on the use surface chaotic flows amenable of mathematical modeling, to fabricate continuous, long and thin filaments of gelatin methacryloyl (GelMA).The fabrication of these filaments is achieved by chaotic advection in a finely controlled and miniaturized version of the journal bearing (JB) system. A drop of GelMA pregel was injected on a higher-density viscous fluid (glycerin) and a chaotic flow is applied through an iterative process. The hydrogel drop is exponentially deformed and elongated to generate a fiber, which was then polymerized under UV-light exposure. Computational fluid dynamic (CFD) simulations are conducted to determine the characteristics of the flow and design the experimental conditions for fabrication of the fibers. GelMA fibers were effectively used as scaffolds for C2C12 myoblast cells. Experimental results demonstrate an accurate accordance with CFD simulations for the predicted length of the fibers.Plant-based viral nanoparticles (i.e., Turnip mosaic virus; TuMV) were then integrated to the hydrogel fibers as a secondary nano-scaffold for cells for enhanced muscle tissue engineering. The addition of TuMV significantly increased the metabolic activity of the cell-seeded fibers (p*<0.05), strengthened cell attachment throughout the first 28 days, improved cell alignment, and promoted the generation of structures that resemble natural mammal muscle tissues.Chaotic 2D-printing is proven to be a viable method for the fabrication of hydrogel fibers. The combined use of thin and long GelMA hydrogel fibers enhanced with flexuous virions offers a promising alternative for scaffolding of muscle cells and show potential to be used as cost-effective models for muscle tissue engineering purposes.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2020

Rapid and cost-effective development of stable clones for the production of anti-Ebola monoclonal antibodies in HEK293T cells

The Ebola virus (EBOV) disease has caused serious and recurrent epidemics in recent years, resulting in a fatality rate of nearly 50%. The most effective experimental therapy against the EBOV is the use of monoclonal antibodies (mAbs). In this work, we describe the development of HEK293T cells engineered for the transient and stable expression of mAb13C6, a neutralizing anti-EBOV monoclonal antibody. We transfected the HEK293T cells with a tricistronic vector to produce the heavy and the light chain of the antibody 13C6 and intracellular Green Fluorescent Protein (GFP) using Lipofectamine 3000. We then selected the transfected cells using puromycin pressure, dilution cloning, and cloning disks. This integrated strategy generated mAb-producing cells in 7 days with a transient expression of [~]1 mg/L. Stable pools were produced after 4 weeks, with expression levels of [~]0.8 mg/L. Stable clones with expression levels of [~]1.8 mg/L were obtained within 10 weeks. The produced antibodies exhibited the expected functionality; they recognized the GP glycoprotein of the Ebola virus in both ELISA assays and cell binding experiments using HEK293T cells engineered to express the EBOV GP at their membrane surface. By the combined use of GFP and the set of selection techniques here described, we drastically reduced the time from transfection to stable clone generation without resorting to costly equipment. In outbreaks or emergencies, this platform can significantly shorten the development of new biopharmaceuticals and vaccines.

bioengineering↗

bioRxiv2019

Using Chaos for Facile High-throughput Fabrication of Ordered Multilayer Micro- and Nanostructures

This paper introduces the concept of continuous chaotic printing, i.e., the use of chaotic flows for deterministic and continuous fabrication of fibers with internal multilayered micro-or nanostructures. Two free-flowing materials are coextruded through a printhead containing a miniaturized Kenics static mixer (KSM) composed of multiple helicoidal elements. This produces a fiber with a well-defined internal multilayer microarchitecture at high speeds (>1.0 m min-1). The number of mixing elements and the printhead diameter determine the number and thickness of the internal lamellae, which are generated according to successive bifurcations that yield a vast amount of inter-material surface area (~102 cm2 cm3) and high resolution features (~10 m). In an exciting further development, we demonstrate a scale-down of the microstructure by 3 orders of magnitude, to the nanoscale level (~10 nm), by feeding the output of a continuous chaotic 3D printhead into an electrospinner. Comparison of experimental and computational results demonstrates the robust and predictable output and performance of continuous chaotic 3D printing. The simplicity and high resolution of continuous chaotic printing strongly supports its potential use in novel applications, including--but not limited to--bioprinting of multi-scale tissue-like structures, modeling of bacterial communities, and fabrication of smart multi-material and multilayered constructs.

bioengineering↗