Genetic Cryopreservation of Rare Breeds of Domesticated North American Livestock: Smithsonian & SVF Biodiversity Preservation Project

Modern agriculture has responded to the growing pressure for animal-protein consumption in the global human population by selecting for specific production traits, which, over the last fifty years, has resulted in a loss of genetic diversity. Most rare and endangered breeds of livestock have not experienced the same selection pressures for production and therefore may contain useful genetic traits not found within modern breeds. In an effort to maintain biodiversity of livestock breeds, the SVF Foundation, a non-profit organization founded to preserve the genetic diversity of food and fiber livestock, has established an ex situ repository of genetic material from endangered North American cattle, sheep, and goats. This genetic material includes in vivo and in vitro produced embryos, semen, fibroblasts, serum, and whole blood DNA cards. The majority of samples in the SVF repository are cryopreserved, creating a genome resource bank for future use. Through the Smithsonian and SVF Biodiversity Preservation Project, this repository will be maintained at the Smithsonian’s Front Royal, VA, facility. This effort represents an excellent model for understanding and sustaining the genetic diversity of rare breeds in the US and in other countries.

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The current state of the problem of in vitrogene pool preservation in poultry

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.611 ◽

2020 ◽

Vol 24 (2) ◽

pp. 176-184

Author(s):

Y. L. Silyukova ◽

O. I. Stanishevskaya ◽

N. V. Dementieva

Keyword(s):

Genetic Diversity ◽

Freeze Drying ◽

Genetic Material ◽

Ex Situ ◽

Farm Animals ◽

Semen Parameters ◽

Embryonic Cells ◽

Current State ◽

Molecular Aspects

This review presents the current progress in and approaches to in vitroconservation of reproductive cells of animals, including birds, such as cryopreservation and freeze-drying, as well as epigenetic conditions for re storing viable spermatozoa and female gametes after conservation. Cryopreservation is an effective way to preserve reproductive cells of various species of animals and birds. In vitrogene pool conservation is aimed primarily to the restoration of extinct breeds and populations and to the support of genetic diversity in populations prone to genetic drift. It is the combination of ex situ in vivoand ex situ in vitromethods that can form the basic principles of the strategy of animal genetic diversity preservation. Also, use of cryopreserved semen allows faster breeding in industrial poultry farming. Despite numerous advances in semen cryobiology, new methods that can more efficiently restore semen fertility after cryopreservation are being sought. The mechanisms underlying the effect of cryopreservation on the semen parameters of cocks are insufficiently understood. The review reflects the results of recent research in the field of cryopreservation of female and male germ cells, embryonic cells, the search for new ways in the field of genetic diversity in vitro (the development of new cryoprotective media and new conservation technologies: freeze-drying). Molecular aspects of cryopreservation and the mechanisms of cryopreservation influence on the epigenetic state of cells are highlighted. Data on the results of studies in the field of male reproductive cell lyophilization are presented. The freeze-drying of reproductive cells, as a technology for cheaper access to the genetic material of wild and domestic animals, compared to cryopreservation, attracts the attention of scientists in Japan, Israel, Egypt, Spain, and France. There is growing interest in the use of lyophilized semen in genetic engineering technologies. Methods of freeze-drying are developed taking into account the species of birds. Organizational and legal ways of solving the problems of in vitroconservation of genetic resources of farm animals, including birds, are proposed.

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Identification of Resistance Determinants for a Promising Antileishmanial Oxaborole Series

Microorganisms ◽

10.3390/microorganisms9071408 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1408

Author(s):

Magali Van den Kerkhof ◽

Philippe Leprohon ◽

Dorien Mabille ◽

Sarah Hendrickx ◽

Lindsay B. Tulloch ◽

...

Keyword(s):

Drug Exposure ◽

In Vitro Selection ◽

Selection Procedure ◽

Cosmid Library ◽

Neglected Diseases ◽

Chromosome 2 ◽

Resistance Determinants ◽

A Genome

Current treatment options for visceral leishmaniasis have several drawbacks, and clinicians are confronted with an increasing number of treatment failures. To overcome this, the Drugs for Neglected Diseases initiative (DNDi) has invested in the development of novel antileishmanial leads, including a very promising class of oxaboroles. The mode of action/resistance of this series to Leishmania is still unknown and may be important for its further development and implementation. Repeated in vivo drug exposure and an in vitro selection procedure on both extracellular promastigote and intracellular amastigote stages were both unable to select for resistance. The use of specific inhibitors for ABC-transporters could not demonstrate the putative involvement of efflux pumps. Selection experiments and inhibitor studies, therefore, suggest that resistance to oxaboroles may not emerge readily in the field. The selection of a genome-wide cosmid library coupled to next-generation sequencing (Cos-seq) was used to identify resistance determinants and putative targets. This resulted in the identification of a highly enriched cosmid, harboring genes of chromosome 2 that confer a subtly increased resistance to the oxaboroles tested. Moderately enriched cosmids encompassing a region of chromosome 34 contained the cleavage and polyadenylation specificity factor (cpsf) gene, encoding the molecular target of several related benzoxaboroles in other organisms.

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CBIO-19. LOW GLOBAL HISTONE H4 ACETYLATION LEVELS REVEAL CANDIDATE QUIESCENT CELL POPULATIONS IN GLIOMA AND DISTINGUISH TUMORS BY GRADE

Neuro-Oncology ◽

10.1093/neuonc/noaa215.079 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii19-ii19

Author(s):

Anca Mihalas ◽

Heather Feldman ◽

Anoop Patel ◽

Patrick Paddison

Keyword(s):

Cell Types ◽

Strand Break ◽

Cell Cycle Gene ◽

Low Grade ◽

Histone H4 ◽

Current Standard ◽

A Genome ◽

Histone H4 Acetylation

Abstract Current standard of care therapy for glioblastoma (GBM) includes cytoreduction followed by ablative therapies that target rapidly dividing cell types. However, the presence of quiescent-like/G0 states, therefore, represents a natural reservoir of tumor cells that are resistant to current treatments. Quiescence or G0 phase is a reversible state of “stasis” cells enter in response to developmental or environmental cues. To gain insight into how glioblastoma cells might regulate G0-like states, we performed a genome-wide CRISPR-Cas9 screen in patient-derived GBM stem-like cells (GSCs) harboring a G0-reporter to identify genes that when inhibited trap GSCs in G0-like states. Among the top screen hits were members of the Tip60/KAT5 histone acetyltransferase complex, which targets both histones (e.g., H4) and non-histone proteins for acetylation. NuA4 functions as a transcriptional activator, whose activities are coordinated with MYC in certain contexts, and also participates in DNA double-strand break repair by facilitating chromatin opening. However, currently little is known about the roles for NuA4 complex in GBM biology. Through modeling KAT5 function in GSC in vitro cultures and in vivo tumors, we find that KAT5 inhibition causes cells to arrest in a G0-like state with high p27 levels, G1-phase DNA content, low protein synthesis rates, low rRNA rates, lower metabolic rate, suppression of cell cycle gene expression, and low histone H4 acetylation. Interestingly, partial inhibition of KAT5 activity slows highly aggressive tumor growth, while increasing p27hi H4-aclow populations. Remarkably, we that low grade gliomas have significantly higher H4-aclow subpopulations and generally lower H4-ac levels than aggressive grade IV tumors. Taken together, our results suggest that NuA4/KAT5 activity may play a key role in quiescence ingress/egress in glioma and that targeting its activity in high grade tumors may effectively “down grade” them, thus, increase patient survival.

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ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1603876113 ◽

2016 ◽

Vol 113 (43) ◽

pp. E6669-E6678 ◽

Cited By ~ 35

Author(s):

Mark A. Gregory ◽

Angelo D’Alessandro ◽

Francesca Alvarez-Calderon ◽

Jihye Kim ◽

Travis Nemkov ◽

...

Keyword(s):

Oxidative Stress ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Mitochondrial Oxidative Stress ◽

Flt3 Inhibitor ◽

A Genome ◽

Flt3 Inhibitors ◽

Acute Myeloid

Activating mutations in FMS-like tyrosine kinase 3 (FLT3) are common in acute myeloid leukemia (AML) and drive leukemic cell growth and survival. Although FLT3 inhibitors have shown considerable promise for the treatment of AML, they ultimately fail to achieve long-term remissions as monotherapy. To identify genetic targets that can sensitize AML cells to killing by FLT3 inhibitors, we performed a genome-wide RNA interference (RNAi)-based screen that identified ATM (ataxia telangiectasia mutated) as being synthetic lethal with FLT3 inhibitor therapy. We found that inactivating ATM or its downstream effector glucose 6-phosphate dehydrogenase (G6PD) sensitizes AML cells to FLT3 inhibitor induced apoptosis. Examination of the cellular metabolome showed that FLT3 inhibition by itself causes profound alterations in central carbon metabolism, resulting in impaired production of the antioxidant factor glutathione, which was further impaired by ATM or G6PD inactivation. Moreover, FLT3 inhibition elicited severe mitochondrial oxidative stress that is causative in apoptosis and is exacerbated by ATM/G6PD inhibition. The use of an agent that intensifies mitochondrial oxidative stress in combination with a FLT3 inhibitor augmented elimination of AML cells in vitro and in vivo, revealing a therapeutic strategy for the improved treatment of FLT3 mutated AML.

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Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow

Blood ◽

10.1182/blood-2010-04-278192 ◽

2010 ◽

Vol 116 (15) ◽

pp. e66-e73 ◽

Cited By ~ 104

Author(s):

Chih-Wen Ni ◽

Haiwei Qiu ◽

Amir Rezvan ◽

Kihwan Kwon ◽

Douglas Nam ◽

...

Keyword(s):

Carotid Artery ◽

Ex Vivo ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Gene Expression Profiles ◽

Disturbed Flow ◽

A Genome ◽

Pattern Comparison

Abstract Recently, we showed that disturbed flow caused by a partial ligation of mouse carotid artery rapidly induces atherosclerosis. Here, we identified mechanosensitive genes in vivo through a genome-wide microarray study using mouse endothelial RNAs isolated from the flow-disturbed left and the undisturbed right common carotid artery. We found 62 and 523 genes that changed significantly by 12 hours and 48 hours after ligation, respectively. The results were validated by quantitative polymerase chain reaction for 44 of 46 tested genes. This array study discovered numerous novel mechanosensitive genes, including Lmo4, klk10, and dhh, while confirming well-known ones, such as Klf2, eNOS, and BMP4. Four genes were further validated for protein, including LMO4, which showed higher expression in mouse aortic arch and in human coronary endothelium in an asymmetric pattern. Comparison of in vivo, ex vivo, and in vitro endothelial gene expression profiles indicates that numerous in vivo mechanosensitive genes appear to be lost or dysregulated during culture. Gene ontology analyses show that disturbed flow regulates genes involved in cell proliferation and morphology by 12 hours, followed by inflammatory and immune responses by 48 hours. Determining the functional importance of these novel mechanosensitive genes may provide important insights into understanding vascular biology and atherosclerosis.

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ETMM-08 METABOLIC REGULATION OF THE EPIGENOME DRIVES LETHAL INFANTILE EPENDYMOMA

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab024.064 ◽

2021 ◽

Vol 3 (Supplement_1) ◽

pp. i15-i16

Author(s):

Sachin Kumar ◽

Antony Michealraj ◽

Leo Kim ◽

Jeremy Rich ◽

Michael Taylor

Keyword(s):

Metabolic Regulation ◽

Primary Cultures ◽

First Trimester ◽

Transcriptional Analysis ◽

Cell Of Origin ◽

H3k27 Trimethylation ◽

A Genome ◽

Rational Therapy

Abstract Ependymomas are malignant glial tumours that occur throughout the central nervous system. Of the nine distinct molecular subgroups of ependymoma, Posterior Fossa A (PFA), is the most prevalent, occurring in the hindbrain of infants and young children. Lacking highly recurrent somatic mutations, PFAs are thought to be a largely epigenetically driven entity, defined by hypomethylation at the histone 3 lysine 27 residue. Previous transcriptional analysis of PFAs revealed an enrichment of hypoxia signaling genes. Thus, we hypothesized that hypoxic signaling, in combination with a unique metabolic milieu, drive PFA oncogenesis through epigenetic regulation. In this study, we identified that PFA cells control the availability of specific metabolites under hypoxic conditions, resulting in diminished H3K27 trimethylation and increased H3K27 acetylation in vitro and in vivo. Unique to PFA cells, transient exposure to ambient oxygen results in irreversible cellular toxicity. Furthermore, perturbation of key metabolic pathways is sufficient to inhibit growth of PFA primary cultures in vitro. PFA cells sequester s-adenosylmethionine while upregulating EZHIP, a polycomb repressive complex 2 (PRC2) inhibitor, resulting in decreased H3K27 trimethylation. Furthermore, hypoxia fine-tunes the abundance of alpha-ketoglutarate and acetyl-CoA to fuel demethylase and acetyltransferase activity. Paradoxically, a genome-wide CRISPR knockout screen identified the core components of PRC2 as uniquely essential in PFAs. Our findings suggest that PFAs thrive in a narrow “Goldilocks” zone, whereby they must maintain a unique epigenome and deviation to increased or decreased H3K27 trimethylation results in diminished cellular fitness. Previously, we showed that PFAs have a putative cell of origin arising in the first trimester of development. Using single-cell RNAseq and metabolomics, we demonstrate that PFAs resemble the natural metabolic-hypoxic milieu of normal development. Therefore, targeting metabolism and/or the epigenome presents a unique opportunity for rational therapy for infants with PFA ependymoma.

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Two Decades of Triazine Dendrimers

Molecules ◽

10.3390/molecules26164774 ◽

2021 ◽

Vol 26 (16) ◽

pp. 4774

Author(s):

Eric E. Simanek

Keyword(s):

Genetic Material ◽

Structural Complexity ◽

Bioactive Molecules ◽

Bioactive Materials ◽

In Vivo Models ◽

Tumor Subtypes ◽

Gas Streams

For two decades, methods for the synthesis and characterization of dendrimers based on [1,3,5]-triazine have been advanced by the group. Motivated by the desire to generate structural complexity on the periphery, initial efforts focused on convergent syntheses, which yielded pure materials to generation three. To obtain larger generations of dendrimers, divergent strategies were pursued using iterative reactions of monomers, sequential additions of triazine and diamines, and ultimately, macromonomers. Strategies for the incorporation of bioactive molecules using non-covalent and covalent strategies have been explored. These bioactive materials included small molecule drugs, peptides, and genetic material. In some cases, these constructs were examined in both in vitro and in vivo models with a focus on targeting prostate tumor subtypes with paclitaxel conjugates. In the materials realm, the use of triazine dendrimers anchored on solid surfaces including smectite clay, silica, mesoporous alumina, polystyrene, and others was explored for the separation of volatile organics from gas streams or the sequestration of atrazine from solution. The combination of these organics with metal nanoparticles has been probed. The goal of this review is to summarize these efforts.

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A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture

eLife ◽

10.7554/elife.51276 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 8

Author(s):

Mark F Sabbagh ◽

Jeremy Nathans

Keyword(s):

Central Nervous System ◽

Endothelial Cells ◽

Nervous System ◽

In Vitro Culture ◽

Vascular Endothelial Cells ◽

Beta Catenin ◽

A Genome ◽

Accessible Chromatin

Vascular endothelial cells (ECs) derived from the central nervous system (CNS) variably lose their unique barrier properties during in vitro culture, hindering the development of robust assays for blood-brain barrier (BBB) function, including drug permeability and extrusion assays. In previous work (Sabbagh et al., 2018) we characterized transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs. In this report, we compare transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs versus mouse CNS ECs in short-term in vitro culture. We observe that standard culture conditions are associated with a rapid and selective loss of BBB transcripts and chromatin features, as well as a greatly reduced level of beta-catenin signaling. Interestingly, forced expression of a stabilized derivative of beta-catenin, which in vivo leads to a partial conversion of non-BBB CNS ECs to a BBB-like state, has little or no effect on gene expression or chromatin accessibility in vitro.

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Features of the preparation of biological material for genome editing in cattle

Agrarian Bulletin of the ◽

10.32417/1997-4868-2019-191-12-40-44 ◽

2019 ◽

Vol 191 (12) ◽

pp. 40-44

Author(s):

A. Barkova ◽

M. Modorov ◽

G. Isaeva ◽

A. Krivonogova

Keyword(s):

Genome Editing ◽

Biological Material ◽

Genetic Material ◽

Cumulus Cells ◽

Vitro Fertilization ◽

Expected Time ◽

Donor Material ◽

Material Transportation

Abstract. To carry out genome editing in cattle, an effective and well-functioning system for obtaining gametes, fertilizing eggs and their cryopreservation is necessary. Aim of the work: review and research of present-day existing methods of obtaining, insemination and cryopreservation of donor material, in order to provide genome editing in cows. Methods and materials. The work is completed according to the theme No. 0532-2019-0001 “Development of complex technology of marker-based genome selection of agricultural animals” within State Order of Ministry of Education and Science of the Russian Federation. The analysis of open scientific literature on the issues of in vitro fertilization in animals, cryopreservation of oocytes and embryons, sperm preparation and methods of insemination of cows’ oocytes, and cryopreservation of oocytes and embryons of animals is done. Features of the preparation of biological material of cattle for genome editing by microinjection into ooplasm are described. Results of research and duscussion. At present time there are two ways to obtain donor material from cattle: from live animals and taking ovaries after slaughtering cows. Material transportation is carried out at a temperature of 30–37 °C depending on the distance to the laboratory and expected time period of transportation. Oocyte-cumulus complexes can be removed by ovarian dissection and aspiration of visible follicles. In both cases, immature eggs are predominantly obtained. Subsequent ripening is carried out in vitro using special media in a CO2 incubator. The culture medium for oocyte maturation should contain hormones that mimic the peak of LH (luteinizing hormone), which occurs in vivo during the maturation of oocytes before ovulation. To accumulate a certain number of eggs at the stage of MII, it is recommended to carry out their cryopreservation by the method of vitrification, having previously released the oocyte from the cumulus cells. After thawing, oocytes need to be incubated for 2–3 hours 38.5 °C in 5–6.5% CO2 to restore the spindle. In order to make editing more effective, the introduction of genetic material is recommended to be carried out in parallel with the fertilization method “icsi”. In humans, mice and rabbits, an injection of sperm into the cytoplasm is sufficient to activate the oocyte, however, in cattle, just micro-injection of the sperm is not enough and often the male pronucleus does not form. To solve the problem, various methods are used, including freezing-thawing of sperm, resulting in damage of a membrane, or addition of heparin-glutathione into the medium that increases decondensation of the sperm DNA.

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Genotoxic potential of nonsteroidal hormones

Veterinarski glasnik ◽

10.2298/vetgl1504245t ◽

2015 ◽

Vol 69 (3-4) ◽

pp. 245-258

Author(s):

Dijana Topalovic ◽

Lada Zivkovic ◽

Ninoslav Djelic ◽

Vladan Bajic ◽

Andrea Cabarkapa ◽

...

Keyword(s):

Oxidative Stress ◽

Genetic Material ◽

Experimental Studies ◽

Genotoxic Effect ◽

Common Mechanism ◽

Genotoxic Effects ◽

Specific Expression ◽

Study Results

Hormones are cellular products involved in the regulation of a large number of processes in living systems, and which by their actions affect the growth, function and metabolism of cells. Considering that hormones are compounds normally present in the organism, it is important to determine if they can, under certain circumstances, lead to genetic changes in the hereditary material. Numerous experimental studies in vitro and in vivo in different systems, from bacteria to mammals, dealt with the mutagenic and genotoxic effects of hormones. This work presents an overview of the research on genotoxic effects of non?steroidal hormones, although possible changes of genetic material under their influence have not still been known enough, and moreover, investigations on their genotoxic influence have given conflicting results. The study results show that mechanisms of genotoxic effect of nonsteroidal hormones are manifested through the increase of oxidative stress by arising reactive oxygen species. A common mechanism of ROS occurence in thyroid hormones and catecholamines is through metabolic oxidation of their phenolic groups. Manifestation of insulin genotoxic effect is based on production of ROS by activation of NADPH isophorms, while testing oxytocin showed absence of genotoxic effect. Considering that the investigations on genotoxicity of nonsteroidal hormones demonstrated both positive and negative results, the explanation of this discordance involve limitations of test systems themselves, different cell types or biological species used in the experiments, different level of reactivity in vitro and in vivo, as well as possible variations in a tissue-specific expression. Integrated, the provided data contribute to better understanding of genotoxic effect of nonsteroidal hormones and point out to the role and mode of action of these hormones in the process of occurring of effects caused by oxidative stress.

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