Dr. Francisco Cruz Sosa
Department of Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa (UAM-Iztapalapa), Mexico.

ISBN 978-93-91473-39-6 (Print)
ISBN 978-93-91473-44-0 (eBook)
DOI: 10.9734/bpi/rrab/v10

This book covers key areas of biological research. The contributions by the authors include B-regulatory cells, adipose tissue derived mesenchymal stromal cells, peripheral blood mononuclear cells, Interleukin-10, lipopolysaccharide E. coli (LPS-EK), flow cytometry, immune-phenotyping, trilateral retinoblastoma, magnetic resonance imaging, genetic screening, developmental biology, rice leaffolder, agent-based models, generalized additive model, history matching, particle swarm optimization algorithm, influenza A virus infection, immune system simulation, apoptosis, necrosis, regulated necrosis, kidney injury, tubular injury, glomerular injury, mitochondria, ischemia-reperfusion injury, proteasome, preservation, organs, inflammation, transplantation, microalgae, antitumoral protein, biomedicine, applied proteomics, industrial application, heterochromatin, molecular cytogenetic mapping, ribosomal genes, translocation factors. This book contains various materials suitable for students, researchers and academicians in the field of biological research.


Optimizing in vitro Generation of Interleukin-10 Secreting B Regulatory Cells

K. S. Gupte, A. V. Vanikar, C. N. Patel, U. G. Thakkar

Recent Research Advances in Biology Vol. 10, 5 July 2021, Page 1-17

A major subset of IL-10 secreting B-cells, commonly characterized as CD19+/38hi/24hi, encompass B-regulatory cells (B-regs). We report effects of changes in stimulating molecule concentration on population of Interleukin-10 secreting B-regs of human origin. B-regs may be obtained from in-vitro co-culture of adipose tissue derived mesenchymal stromal cells (AD-MSC) and peripheral blood mononuclear cells (PBMC) for potential cell therapy. Lipopolysaccharide–E.coli-K12 strain (LPS-EK) was added in varying concentrations in the co-culture of AD-MSC and peripheral blood mononuclear cells (PBMC). At each time point, IL-10 concentration of cell supernatant was estimated by quantitative ELISA. Morphology, sterility, total count, viability and immune-phenotype of cells were determined. We analyzed the data to determine the time interval at which maximum B-reg population and optimum secretion of IL-10 was obtained. The present study provides precious information about the in vitro dynamics of IL-10 secretion by human B-regs generated from AD-MSC and PBMC. The present study focuses on in vitro generation of B-regs from adipose tissue derived mesenchymal stromal cells (AD-MSC) and peripheral blood mononuclear cells (PBMC), as well as on partial characterization of B-regs in terms of amount of IL-10 secreted, time taken and amount of stimulating molecule (i.e. LPS-EK) required for optimum IL-10 secretion. It has been reported that B-regs secrete cytokine in trace quantities. The medium which is added for feeding the cells further dilutes the secreted cytokines by many folds. In our study, the samples were appropriately concentrated, so that the cytokines could be detected by quantitative Enzyme Linked Immunosorbent Assay (ELISA).

The trilateral retinoblastoma is the heritable form of retinoblastoma associated with an intracranial tumor that most effect the pineal gland, as well as the suprasellar or intrasellar region of the brain. Because of this rarity, few works on the molecular genetics of this tumor has been reported being important the report of these cases associated with molecular studies. This work aims to alert health professionals to the early diagnosis of retinoblastoma, and to highlight the use of intracranial magnetic resonance imaging to track secondary tumors, including trilateral retinoblastoma. More than 50% of trilateral retinoblastoma is diagnosed at the time of retinoblastoma diagnosis by magnetic resonance imaging, suggesting that baseline screening for trilateral retinoblastoma might indeed be useful. In this paper, we present three cases of trilateral retinoblastoma with diagnosis obtained by magnetic resonance imaging and the molecular data found for each proband.

Cardiochiles nigricollis Cameron is a larval endo-parasitoid of the two rice leaf folder species, Cnaphalocrocis medinalis (Guenee) and Marasmia exigua Butler. Developmental biology of C. nigricollis was studied on the host C. medinalis. Usually third and fourth instar larvae of the leaffolder species were parasitized by the parasitoid. During the development of the parasitoid, four instars were discovered. The larvae of the first instar are segmented and slightly bent. Segmentation appeared in the second instar, and the tracheal system could be seen faintly. The head was clearly defined in the third instar, and the larva expanded in size. The full-grown larva emerged from the host six to eight days after the egg was laid. Females had a 5.3-day pupal period and males had a 6.7-day pupal period on average. Incubation time, larval time, and pupal time were all 1.2 days, 10 days, and 6.7 days, respectively. C. nigricollis went into diapause at the pupal stage, which began in late August and grew gradually until the first week of December, when the entire population went into diapause. This phenomena was only noticed during the rainy season. Males emerged after 213 days on average, and females after 224 days from diapausing pupae. The steady increase in the number of C. nigricollis entering diapause in the field population could be attributed to the presence of a heterogeneous population of C. nigricollis in the field that responded to changes in air temperature over time. Brachymeria sp., Orgilus sp., Trichomalopsis (Eupteromalus) parnarae Gahan and Elasmus sp. were reared as hyper-parasitoids on pupae of C. nigricollis.

Since they can provide a natural and flexible description of nonlinear dynamic behavior of complex system, Agent-based models (ABM) have been commonly used for immune system simulation. However, it is crucial for ABM to obtain an appropriate estimation for the key parameters of the model by incorporating experimental data. In this paper, a systematic procedure for immune system simulation by integrating the ABM and regression method under the framework of history matching is developed. A novel parameter estimation method by incorporating the experiment data for the simulator ABM during the procedure is proposed. First, we employ ABM as simulator to simulate the immune system. Then, the dimension-reduced type generalized additive model (GAM) is employed to train a statistical regression model by using the input and output data of ABM and play a role as an emulator during history matching. Next, we reduce the input space of parameters by introducing an implausible measure to discard the implausible input values. At last, the estimation of model parameters is obtained using the particle swarm optimization algorithm (PSO) by fitting the experiment data among the non-implausible input values. The real Influeza A Virus (IAV) data set is employed to demonstrate the performance of our proposed method, and the results show that the proposed method not only has good fitting and predicting accuracy, but it also owns favorable computational efficiency.

Cell Death and Organ Injury: The Example of the Kidney

Giovanna Priante, Lisa Gianesello, Monica Ceol, Dorella Del Prete, Franca Anglani

Recent Research Advances in Biology Vol. 10, 5 July 2021, Page 46-82

When tissues are damaged, they usually heal. The cellular responses towards healing require the prior recognition that damage has occurred. Apoptotic cell death is usually a response to the cell’s microenvironment. In fact, prolonged cellular stress may activate homeostatic repair processes, or cells may undergo apoptosis when overwhelmed by the stress.

In the kidney apoptosis contributes to parenchymal cell loss in the course of acute and chronic renal injury, but does not trigger an inflammatory response. On the contrary if inflammation happens, we can have necrosis which differs from apoptosis by the breakdown of integrity of the plasma membrane so necrotic cell death is accompanied by the release of unprocessed intracellular content, including cellular organelles, which are highly immunogenic proteins. The relative contribution of apoptosis and necrosis to injury varies, depending on the severity of the insult. Regulated cell death may result from immunologically silent apoptosis or from immunogenic necrosis. Recent advances have enhanced the most revolutionary concept of regulated necrosis. Several modalities of regulated necrosis have been described, such as necroptosis, ferroptosis, pyroptosis, parhanatos, mitochondria permeability transition regulated necrosis and NETosis. In cell death, mitochondria, which are widely known for their canonical role in cellular respiration and oxidative phosphorylation, are also recognized as key contributors in the cell death pathway, with a central role in detecting and integrating signals from the environment to trigger adaptive and compensatory responses in cells. Thus, mitochondrial damage and dysfunction are identified as one of the pathogenic events in a variety of diseases, including both chronic and acute kidney diseases. Therefore, we review the different modalities of cell death in kidney injury, pointing in particular to converging pathways of cell death and evidencing that a combination therapy targeting multiple cell-death pathways may lead to new opportunities for therapeutic intervention.

The shortage of donor organs is a major global concern. Organ failure requires the transplantation of functional organs. Donor’s organs are preserved for variable periods of warm and cold ischemia time, which requires placing them into a preservation device. Ischemia and reperfusion damage the organs, due to the lack of oxygen during the ischemia step, as well as the oxidative stress during the reperfusion step. Different methodologies are developed to prevent or to diminish the level of injuries. Preservation solutions were first developed to maximize cold static preservation, which includes the addition of several chemical compounds. The next chapter of organ preservation comes with the perfusion machine, where mechanical devices provide continuous flow and oxygenation ex vivo to the organs being preserved. In the addition of inhibitors of mitogen-activated protein kinase and inhibitors of the proteasome, mesenchymal stem cells began being used 13 years ago to prevent or diminish the organ’s injuries. Mesenchymal stem cells (e.g., bone marrow stem cells, adipose derived stem cells and umbilical cord stem cells) have proven to be powerful tools in repairing damaged organs. This review will focus upon the use of some bone marrow stem cells, adipose-derived stem cells and umbilical cord stem cells on preventing or decreasing the injuries due to ischemia-reperfusion.

Proteasome and Organs Ischemia-Reperfusion Injury: A Review

Joan Oliva

Recent Research Advances in Biology Vol. 10, 5 July 2021, Page 103-118

The treatment of organ failure on patients requires the transplantation of functional organs, from donors. Over time, the methodology of transplantation was improved by the development of organ preservation solutions. The storage of organs in preservation solutions is followed by the ischemia of the organ, resulting in a shortage of oxygen and nutrients, which damage the tissues. When the organ is ready for the transplantation, the reperfusion of the organ induces an increase of the oxidative stress, endoplasmic reticulum stress, and inflammation which causes tissue damage, resulting in a decrease of the transplantation success. However, the addition of proteasome inhibitor in the preservation solution alleviated the injuries due to the ischemia-reperfusion process. The proteasome is a protein structure involved in the regulation the inflammation and the clearance of damaged proteins. The goal of this review is to summarize the role of the proteasome and pharmacological compounds that regulate the proteasome in protecting the organs from the ischemia-reperfusion injury.

Nannochloropsis gaditana as a Source of Novel Antitumor Compounds

Carrasco-Reinado, Rafael, Escobar-Niño, Almudena, Fernández-Acero, Francisco Javier

Recent Research Advances in Biology Vol. 10, 5 July 2021, Page 119-136

During the last decades, proteomics approaches has become in a fundamental tool to unravel the proteins dynamic of biological processes, being an essential technique for basic and applied research [1-4]. Diverse bioinformatic tools are required to manage and explore the huge amount of information obtained from a single proteomics experiment.  To gain insight into potential applications of the identified proteins, a novel approach named "Applied Proteomics" has been developed by comparing the obtained protein information with the existing patents database.

The development of massive sequencing technology and MS/MS improvements has allowed the application of proteomic of non-model microorganisms, which have been deeply described as a novel source of metabolites [5-8]. Between them, Nannochloropsis gaditana that has been pointed out as an alternative source of biomolecules [9-13]. Recently, our research group has reported the first complete proteome analysis of this microalga [14], which was analysed using the applied proteomics concept with the identification of 488 proteins with potential industrial applications. To validate our approach, we select UCA01 protein from prohibitin family. The recombinant protein showed its antitumor activity against two tumor cell lines, Caco2 (colon adenocarcinoma) and HepG-2 (hepatocellular carcinoma), proving that proteome data has been transformed into relevant biotechnological information.

In summary, the framework of the European Union “Blue growth” politicies, the revalorization of microalgae biomass is crucial point. From Nannochloropsis gaditana has been developed a new tool against cancer, the protein named UCA01. This protein has selective effect inhibiting the growth of tumour cells, while does not show any effect over control cells. This approach describes the first practical approach to transform proteome information in a potential industrial application, named “applied proteomics”. It is based in a novel bio-algorism, which is able to identified proteins with potential industrial applications. From hundreds of proteins described in the proteome of N. gaditana, the bio-algorism identified over 400 proteins with potential use; one of them was selected as UCA01, “in vitro” and its potential prove it against cancer. The potential applications from this approach are unpredictable.

Objective: The main objective of this study is to analyze the heterochromatin (DNA sequences non-coding rich in CG base) genomes of a primary triticale, and their progenitors, wheat and rye on the one hand, and on the other to Localizes the nuclear organizer regions (NOR) and ribosomal genes (5S and 45S).

Methodology and Results: The Analysis of C bands of genomes the hybrids are in a comparison with their genitors displayed a different marking. In the genomes A, hybrid (Mahon-demiasxRC9) is less heterochromatic than the genitor D (Mahon-demias). The genomes B and D of the hybrid (Mahon-demias xRC9) show a richness in heterochromatin relative to their homologous of the D genitor. Nevertheless, in R genome of hybrid (Mahondemias xRC9) is almost similar to its E genitor (RC9), except the 2BL / 7RS chromosome. In the genitors and in the hybrids, the organizing regions (NOR) marked on the chromosomes 1R, 2R, 3R and 6R of rye and on the chromosome 1B of wheat and on the chromosomes 1B, 1R, 2R, 3R, 6R of triticale, showed the same localization compared with that is described by authors. The molecular analysis shows that, 5S locus is co-localized with the 45S locus on the chromosome 5R. The 45S loci are located on the 1R, 3R, 5R and 7R chromosomes. They correspond to the nuclear organizer regions (N.O.R). While in triticale, 5S loci are located on chromosomes 2A, 5B and 7RS / 2BL. The 45S locus is located on chromosomes 1R, 3R and 7RS / 2BL. Contrary to the bibliography, the chromosome 5R shows two loci 5S and 45S co localized on the telomer of the short arm. This result suggests that the variety of rye that served as genitor acquired during its selection of rDNA that it transmits to his descendants in a stable manner. 7RS / 2BL Translocation highlighted by C-banding is confirmed by FISH.

Conclusion and Application of Results: The results indicate the existence of intervarietal and interspecific polymorphisms in rye and triticale, as well as the presence of chromosomes B of telocentric form or isochromosomes a heterochromatic and / or euchromatic structure. In a conclusion, we establish a molecular cytogenetic mapping of marker chromosomes and ribosomal genes of our vegetal material (genitors and hybrid).