Triku: a feature selection method based on nearest neighbors for single-cell data

Abstract BACKGROUND: Feature selection is a relevant step in the analysis of single-cell RNA sequencing datasets. Most of the current feature selection methods are based on general univariate descriptors of the data such as the dispersion or the percentage of zeros. Despite the use of correction methods, the generality of these feature selection methods biases the genes selected towards highly expressed genes, instead of the genes defining the cell populations of the dataset. RESULTS: Triku is a feature selection method that favors genes defining the main cell populations. It does so by selecting genes expressed by groups of cells that are close in the k-nearest neighbor graph. The expression of these genes is higher than the expected expression if the k-cells were chosen at random. Triku efficiently recovers cell populations present in artificial and biological benchmarking datasets, based on adjusted Rand index, normalized mutual information, supervised classification, and silhouette coefficient measurements. Additionally, gene sets selected by triku are more likely to be related to relevant Gene Ontology terms and contain fewer ribosomal and mitochondrial genes. CONCLUSION: Triku is developed in Python 3 and is available at https://github.com/alexmascension/triku.This work was supported by grants from Instituto de Salud Carlos III (AC17/00012 and PI19/01621), cofunded by the Euro- pean Union (European Regional Development Fund/European Sci- ence Foundation, Investing in your future) and the 4D-HEALING project (ERA-Net program EracoSysMed, JTC-2 2017); Diputación Foral de Gipuzkoa, and the Department of Economic Devel- opment and Infrastructures of the Basque Government (KK- 2019/00006, KK-2019/00093); European Union FET project Cir- cular Vision (H2020-FETOPEN, Project 899417), Ministry of Sci- ence and Innovation of Spain; and PID2020-119715GB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe. A.M.A. was supported by a Basque Govern- ment Postgraduate Diploma fellowship (PRE_2020_2_0081), and O.I.S. was supported by a Postgraduate Diploma fellowship from la Caixa Foundation (identification document 100010434; code LCF/BQ/IN18/11660065)

Physicochemical and Biological Performance of Aloe Vera-Incorporated Native Collagen Films

Collagen was obtained from porcine skin by mechanical pretreatments with the aim of preserving the triple helix structure of native collagen, which was indirectly corroborated by differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR) results. Moreover, aloe vera (AV), with inherent biological properties, was incorporated into collagen film formulations, and films were prepared by compression and characterized to assess their suitability for biomedical applications. SEM images showed that the fibrillar structure of collagen changed to a rougher structure with the addition of AV, in accordance with the decrease in the lateral packaging of collagen chains observed by XRD analysis. These results suggested interactions between collagen and AV, as observed by FTIR. Considering that AV content higher than 20 wt % did not promote further interactions, this formulation was employed for biological assays and the suitability of AV/collagen films developed for biomedical applications was confirmed.This research was funded by the Basque Government, grant number KK-2019/00006

Combination of 3D printing and electrospinning to develop chitin/gelatin/PVA scaffolds

In this study, novel scaffolds based on natural polymers were developed by combining 3D printing (3DP) and electrospinning (ES) techniques. ES ink was prepared with gelatin and poly(vinyl alcohol) (PVA), while 3DP ink was prepared with gelatin and chitin. Different biopolymers were used to confer unique properties to each ink and obtain a multilayered scaffold suitable for tissue regeneration. First, gelatin is able to exhibit the characteristics needed for both inks since gelatin chains contain arginineglycine-aspartic (RGD) motifs, an important sequence in the promotion of cell adhesion, which gives gelatin an improved biological behavior in comparison to other polymers. Additionally, PVA was selected for ES ink to facilitate gelatin spinnability, and chitin was incorporated into 3DP ink as reinforcement to provide mechanical support and protection to the overall design. In this work, chitin was extracted from fruit fly pupae. The high extraction yield and purity of the chitin obtained from the fruit fly pupae confirmed that this pupa is an alternative source to produce chitin. Once the chitin was characterized, both inks were prepared and rheological analysis was carried out in order to confirm the shear thinning behavior required for additive manufacturing processes. The combination of 3DP and ES processes resulted in porous scaffolds, which were proven biocompatible, highlighting their potential for biomedical applications.This work was supported by the Basque Government through the research groups of the Basque university system (IT1658-22) and through Elkartek Program (KK- 2022/00019). Work at Biodonostia was supported by Project PI19/01621, funded by Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union. J.U. thanks the University of the Basque Country (ESPDOC21/74).T.C. (PRE_2021_1_0254) and A.I. (PRE_2019_1_0031) thank the Basque Government for their fellowships

A Green Approach towards Native Collagen Scaffolds: Environmental and Physicochemical Assessment

Native collagen scaffolds were prepared in this work, in which both materials and environmental approaches were considered with the aim of providing a global strategy towards more sustainable biomaterials. From the environmental perspective, it is worth mentioning that acid and enzymatic treatments have been avoided to extract collagen, allowing the reduction in the use of resources, in terms of chemicals, energy, and time, and leading to a low environmental load of this step in all the impact categories under analysis. With the incorporation of chitosan into the scaffold-forming formulations, physical interactions occurred between collagen and chitosan, but the native collagen structure was preserved, as observed by Fourier transform infrared (FTIR) and X-ray diffraction (XRD) analyses. The incorporation of chitosan also led to more homogenous porous microstructures, with higher elastic moduli and compression resistance for both dry and hydrated scaffolds. Furthermore, hydrated scaffolds preserved their size and shape after some compression cycles.This research was funded by the Ministry of Science, Innovation and Universities (RTI2018-097100-B-C22) and the Basque Government (38-2018-00037). M.A. (PRE_2017_1_0025) and A.Ir. (PRE_2019_1_0031) thank the Basque Government for their fellowships

Human Hair Follicle-Derived Mesenchymal Stromal Cells from the Lower Dermal Sheath as a Competitive Alternative for Immunomodulation

Mesenchymal stromal cells (MSCs) have unique immunomodulatory capacities. We investigated hair follicle-derived MSCs (HF-MSCs) from the dermal sheath, which are advantageous as an alternative source because of their relatively painless and minimally risky extraction procedure. These cells expressed neural markers upon isolation and maintained stemness for a minimum of 10 passages. Furthermore, HF-MSCs showed responsiveness to pro-inflammatory environments by expressing type-II major histocompatibility complex antigens (MHC)-II to a lesser extent than adipose tissue-derived MSCs (AT-MSCs). HF-MSCs effectively inhibited the proliferation of peripheral blood mononuclear cells equivalently to AT-MSCs. Additionally, HF-MSCs promoted the induction of CD4+CD25+FOXP3+ regulatory T cells to the same extent as AT-MSCs. Finally, HF-MSCs, more so than AT-MSCs, skewed M0 and M1 macrophages towards M2 phenotypes, with upregulation of typical M2 markers CD163 and CD206 and downregulation of M1 markers such as CD64, CD86, and MHC-II. Thus, we conclude that HF-MSCs are a promising source for immunomodulation.This work was supported by the projects SAF2017-82292-R (MINECO), MCIU-AEI/ FEDER, UE, ICTS “NANBIOSIS” Drug Formulation Unit (U10) and the Eusko Jaurlaritza (Grupos Consolidados, No ref: IT907-16)

Isolation and characterization of myogenic precursor cells from human cremaster muscle

Human myogenic precursor cells have been isolated and expanded from a number of skeletal muscles, but alternative donor biopsy sites must be sought after in diseases where muscle damage is widespread. Biopsy sites must be relatively accessible, and the biopsied muscle dispensable. Here, we aimed to histologically characterize the cremaster muscle with regard number of satellite cells and regenerative fibres, and to isolate and characterize human cremaster muscle-derived stem/precursor cells in adult male donors with the objective of characterizing this muscle as a novel source of myogenic precursor cells. Cremaster muscle biopsies (or adjacent non-muscle tissue for negative controls; N=19) were taken from male patients undergoing routine surgery for urogenital pathology. Myosphere cultures were derived and tested for their in vitro and in vivo myogenic differentiation and muscle regeneration capacities. Cremaster-derived myogenic precursor cells were maintained by myosphere culture and efficiently differentiated to myotubes in adhesion culture. Upon transplantation to an immunocompromised mouse model of cardiotoxin-induced acute muscle damage, human cremaster-derived myogenic precursor cells survived to the transplants and contributed to muscle regeneration. These precursors are a good candidate for cell therapy approaches of skeletal muscle. Due to their location and developmental origin, we propose that they might be best suited for regeneration of the rhabdosphincter in patients undergoing stress urinary incontinence after radical prostatectomy.We thank patients and medical personnel for their generous involvement in the study. We also acknowledge the help of Biodonostia Animal and Experimental Operations Facility. This work was supported by grants from Ministerio de Economia y Competitividad (RTC-2015-3750-1) and Instituto de Salud Carlos III (PI13/02172, PI16/01430) to A.I., co-funded by the European Union (ERDF/ESF, 'Investing in your future'). N.N.-G. received a studentship from the Department of Education, University and Research of the Basque Government (PRE2013-1-1168). A.L.M. was funded by grants from FIS (PI17/01841 and PI14/00436), CIBERNED and the Basque Government (2015/11038, RIS3 2017222021 and BIO16/ER/022). M.F.L.-C. was supported by the Servicio Andaluz de Salud from the Consejeria de Salud de la Junta de Andalucia, grant PI 0222-2014, co-funded by the European Union (ERDF/ESF). I.M.A was funded by grants from Ministerio de Economia y Competitividad (PEJ-2014-P-01215 and FJCI-2016-28121)

Replicación y encapsidación de minigenomas RNA derivados de coronavirus. Expresión de genes heterólogos

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 05-10-200