Choice of Explant for Plant Genetic Transformation

Particle bombardment or biolistic transformation is an efficient, versatile method. This method does not need any vector for the gene transfer and is not dependent on the cell type, species, and genotype. The success of any transformation technique depends on the starting experimental materials or the explants. Here, we describe the factors that have influenced the choice of explants in biolistic transformation. Many general factors in the selection of explants in the development of transgenic plants are presented here. Therefore, this chapter provides extensive guidelines regarding the choice of explants for researchers working on various plant genetic transformation techniques.

From cells highly tolerant to Zn and Pb to fully fertile plants - Selection of tolerant lines with in vitro culture

Viola arvensis cells were selected after treatment with Zn or Pb and regenerated into plants likely to have higher tolerance levels than the initial plant. The surviving cells in the suspension treated with 2000 μM of Zn, 2000 μM of Pb or 0 μM for 72 h were maintained on a solidified half-strength MS medium supplemented with 0.5 mg L^-1 TDZ to induce divisions and organogenesis. The adventitious shoots obtained were rooted on a half-strength MS medium with 1 mg L^-1 IBA. Regenerants derived from the Zn- and Pb-treated cells were vigorous and fully fertile. The in vitro conditions and metal impact generated a low genome alteration and overall low genetic diversity of regenerants compared to the initial plant and plants from the natural population. The cells of regenerants obtained after Pb treatment represented an approximately 12% higher tolerance level to Pb than the cells of the initial plant. This is the first report of plant regeneration from highly tolerant cells selected by heavy metal treatment. Regenerants successfully obtained in vitro could be considered as a source material for the recultivation of areas polluted with heavy metals.

An efficient in vitro regeneration system from different wild apple (Malus sieversii) explants

BACKGROUND

Wild apple, Malus sieversii, is an endangered species and a valuable genetic resource that requires a variety of conservation techniques. This study aimed to investigate the influence of different concentrations of hormones on wild apple regeneration from leaf and stem explants to establish an optimal regeneration system.

RESULTS

Leaves and stems derived from seedlings were cultured on several media supplemented with various concentrations of thidiazuron (TDZ) or 6-benzylaminopurine (BA) in different combinations with 1-naphthaleneacetic acid (NAA). The results showed that the most efficient shoot formation media (35% and 90%) were MS medium containing 4.0 mg L^-1 TDZ and 1.0 mg L^-1 NAA for leaf explants and MS medium containing 1.0 mg L^-1 BA without NAA for stem explant. MS medium supplemented with 0.4 mg L^-1 BA and 0.1 mg L^-1 NAA (for shoot multiplication) and 1/2 MS + 0.1 mg L^-1 NAA + 1.5% sucrose (for rooting) were effective media. Shoot regeneration from leaf explants was the most effective when the explants were placed abaxial side down onto the medium and were subjected to a pre-treatment of 3 weeks in darkness.

CONCLUSIONS

An optimized regeneration system for M. sieversii that allowed regeneration within 2-3 months developed. The protocol developed herein can be used in large-scale clonal propagation for the conservation of wild apple, M. sieversii.

Biolistic DNA Delivery and Its Applications in Sorghum bicolor

Biolistic DNA delivery has been considered a universal tool for genetic manipulation to transfer exotic genes to cells or tissues due to its simplicity, versatility, and high efficiency. It has been a preferred method for investigating plant gene function in most monocot crops. The first transgenic sorghum plants were successfully regenerated through biolistic DNA delivery in 1993, with a relatively low transformation efficiency of 0.3%. Since then, tremendous progress has been made in recent years where the highest transformation efficiency was reported at 46.6%. Overall, the successful biolistic DNA delivery system is credited to three fundamental cornerstones: robust tissue culture system, effective gene expression in sorghum, and optimal parameters of DNA delivery. In this chapter, the history, application, and current development of biolistic DNA delivery in sorghum are reviewed, and the prospect of sorghum genetic engineering is discussed.

Endometrial cancer and its cell lines

Endometrial cancer is one of the most common gynaecological malignancies worldwide. One type of research in this field is the growing of cell lines (CLs) and cultures, which can be used to explore the biological mechanisms of cancer. The purpose of this review is to offer an overview of the current literature and highlight the importance of correct CL studies. We carried out a literature analysis of more than 60 articles from the Pubmed, Medline databases that were almost exclusively published in indexed journals in the last 10 years as well as the primary originating scientific studies of specific CLs. We then summarized the newest findings and recommendations. Cell lines are becoming widely used as in vitro tumour models. Recent work has shown inconsistencies in nomenclature and culturing of CLs. Their genomic evolution leads to a high degree of variation across CL strains therefore it is of the utmost importance to recognize the variability within laboratory cancer models. Laboratories must adapt, incorporate additional characterisation techniques and view this situation as an opportunity to improve the reproducibility of pre-clinical cancer research. The authors offer a comprehensive literature review about endometrial cancer CLs, a review of the current literature and advice on culturing CLs.

Preparation of osteogenic matrices from cultured cells

Bone is a composite material consisting primarily of cells, extracellular matrices, accessory proteins and the complex calcium phosphate salt hydroxyapatite. Collectively, the extracellular network of proteins and accessory molecules that provide the organic component of bone tissue is referred to as the osteogenic extracellular matrix (OECM). OECM provides tensile strength and increases the durability of bone, but the OECM also serves as an attachment site and regulatory substrate for cells and a repository for growth factors and cytokines. Increasingly, purified OECM generated by osteogenic cells in culture has attracted interest because it has the capacity to improve the growth and viability of attached cells, enhances the osteogenic program in vitro and in vivo, and shows great promise as a therapeutic tool for orthopedic tissue engineering. This chapter will describe fundamental protocols for the selection and culture of osteogenic cells and conditions for their osteogenic differentiation, and the synthesis, purification and characterization of OECM. Some examples of immobilization to surfaces for the purpose of two- and three-dimensional culture will also be described.

The impact of cryopreservation on bone marrow-derived mesenchymal stem cells: a systematic review

Mesenchymal stem cells (MSCs) represent an invaluable asset for the field of cell therapy. Human Bone marrow-derived MSCs (hBM-MSCs) are one of the most commonly used cell types in clinical trials. They are currently being studied and tested for the treatment of a wide range of diseases and conditions. The future availability of MSCs therapies to the public will require a robust and reliable delivery process. Cryopreservation represents the gold standard in cell storage and transportation, but its effect on BM-MSCs is still not well established. A systematic review was conducted to evaluate the impact of cryopreservation on BM-MSCs and to attempt to uncover the reasons behind some of the controversial results reported in the literature. Forty-one in vitro studies were analysed, and their results organised according to the cell attributes they assess. It was concluded that cryopreservation does not affect BM-MSCs morphology, surface marker expression, differentiation or proliferation potential. However, mixed results exist regarding the effect on colony forming ability and the effects on viability, attachment and migration, genomic stability and paracrine function are undefined mainly due to the huge variabilities governing the cryopreservation process as a whole and to the lack of standardised assays.

Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

BACKGROUND

Plant height is one of the most important agronomic traits in many crops due to its influence on lodging resistance and yield performance. Although progress has been made in the use of dwarfing genes in crop improvement, identification of new dwarf germplasm is still of significant interest for breeding varieties with increased yield.

RESULTS

Here we describe a dominant, dwarf mutant G7 of Brassica napus with down-curved leaves derived from tissue culture. To explore the genetic variation responsible for the dwarf phenotype, the mutant was crossed to a conventional line to develop a segregating F₂ population. Bulks were formed from plants with either dwarf or conventional plant height and subjected to high throughput sequencing analysis via mutation mapping (MutMap). The dwarf mutation was mapped to a 0.6 Mb interval of B. napus chromosome C05. Candidate gene analysis revealed that one SNP causing an amino acid change in the domain II of Bna.IAA7.C05 may contribute to the dwarf phenotype. This is consistent with the phenotype of a gain-of-function indole-3-acetic acid (iaa) mutant in Bna.IAA7.C05 reported recently. GO and KEGG analysis of RNA-seq data revealed the down-regulation of auxin related genes, including many other IAA and small up regulated response (SAUR) genes, in the dwarf mutant.

CONCLUSION

Our studies characterize a new allele of Bna.IAA7.C05 responsible for the dwarf mutant generated from tissue culture. This may provide a valuable genetic resource for breeding for lodging resistance and compact plant stature in B. napus.

Safety assessment of antibiotic administration by magnetic nanoparticles in in vitro zebrafish liver and intestine cultures

Different in vitro models have been suggested to replace in vivo studies. In vitro studies are of great interest and give the opportunity to analyze cellular responses in a closed system with stable experimental conditions and to avoid direct animal exposure and distress during the experiments. These methods are useful to test drugs and chemicals toxicity in order to better understand their environmental impact. In the present study, fish organ cultures have been used to test different oxytetracycline exposure methods, including oxide nanoparticles (IONPs), using zebrafish as experimental model. Results showed that oxytetracycline accumulation at the end of the experiment (24 h) in the exposed organs did not show any significant difference in the analyzed samples and was not dependent on the exposure way (free or IONPs-bound oxytetracycline). However, as regards molecular analysis, the different exposure ways tested in this study showed some differences in the expression of genes involved in stress response. The present data did not completely agree with a previous in vivo study performed in zebrafish using IONPs, underlying that replacement of in vivo models with in vitro studies cannot always represent the complexity of interactions typical of a biological system.

Changes in DNA methylation pattern of apple long-term in vitro shoot culture and acclimatized plants

DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material, and the average level of DNA methylation was 49.77%, 34.65% and 8.77% in CpG, CHG and CHH contexts, respectively. Significant differences in DNA methylation were identified in 586 (specifically 334, 201 and 131 in CpG, CHG and CHH contexts, respectively) out of 45,116 genes, including promoter and coding sequences. These were classified as differentially methylated genes (DMGs). This is a 1.3% difference in the level of DNA methylation of genes in response to a change in the environment. Differential methylation was visualised by MA plots and functional genomic maps were established for biological processes, molecular functions and cellular components. When the DMGs were considered, in vitro tissue culture resulted in the highest level of methylation, but it was lower in acclimatized in vitro plants which was similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2 GO v5.1.12 for Gene Ontology. DMGs identified as MD07G1113000 (protein transport), MD08G1041600 (extracellular space), MD09G1054800 (phosphatidic acid binding), and MD10G1265800 (not annotated) were methylated in all three contexts in in vitro shoots. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying the epigenome and thereby gene expression.

Use of in vitro electroporation and slice culture for gene function analysis in the mouse embryonic spinal cord

The spinal cord is an important part of the central nervous system (CNS). At present, the expression of the exogenous gene in the spinal cord of the embryonic mouse needs in utero spinal cord electroporation, but the success rate of this technique is very low. In this study, we have demonstrated the expression of an exogenous gene on one side of the spinal cord by combining two methods-in vitro electroporation of embryonic mouse spinal cord and organ spinal cord slices culture. We took 12-day embryonic mice, injected the green fluorescent protein (pCAGGS-GFP) plasmid into the spinal cord cavity in vitro, and then electroporated. The spinal cord was cut into 300-μm slices using a vibratory microtome. After cultured for 48 h, GFP-positive neurons were clearly observed on one side of the spinal cord, indicating that the exogenous gene was successfully transferred. The axon projection direction is basically unanimous from the inside to the lateral edge of the spinal cord. Compared to neurons in vivo, a single neuron in the culturing section has more complete neurites and is conducive to studying changes in the structure and behavior of individual neurons. Based on the above results, we have successfully established a convenient and efficient method for expressing the exogenous gene in the spinal cord of the mouse.

In vitro osteodifferentiation of intact human amniotic membrane is not beneficial in the context of bone repair

The human amniotic membrane (hAM) is an attractive biomaterial for regenerative medicine, as it contains amniotic mesenchymal stromal cells (hAMSC), epithelial cells (hAEC) and growth factors. We examined the potential use of hAM in orthopaedic and maxillofacial bone surgery, integrating the requirements of current regulations regarding advanced therapy medicinal products (ATMP) in the European Union. Previous studies have described the potential osteodifferentiation of intact hAM during whole-tissue culture in osteogenic conditions. The present study aims to determine whether in vitro osteodifferentiation of hAM is needed in the context bone repair, and the influence of this process on tissue structure, cell phenotype and cell function. Different conditions (fresh or cultured hAM; intact or hAM-derived cells) were tested. Phenotypic and functional analyses were performed with standard approaches (cell culture and staining, histological and immunolabelling) as well as original approaches (tissue staining, energy dispersive X-ray and X-ray diffraction). In our study, non-osteodifferentiated hAM (i.e., fresh or native hAM) exhibited innate pre-osteoblastic potential. Osteodifferentiation of fresh hAM induced a change in tissue structure, cell phenotype and function. Therefore, we hypothesize that pre-osteodifferentiation may not be necessary, especially if it induces unwanted changes. To our surprise, in these osteogenic conditions, hAEC had a mesenchymal phenotype with osteocyte function, and even native synthesis of hydroxyapatite, focusing osteogenic potential mainly in this epithelial layer. In conclusion, in vitro osteodifferentiation by tissue culture does not appear to be necessary for hAM to be used as an innovative ATMP for bone repair.

What Can Cell Culture Systems Reveal About Sieve Element Differentiation?

Tissue culture systems can be powerful tools for studying the process of cell differentiation in detail. Although a large number of cultures for xylem differentiation have been developed and utilized, there are only few reports on culture systems for ectopic phloem differentiation. Recently, a novel tissue culture system named Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL) was established, in which both xylem and phloem cells can be rapidly and efficiently induced in the model plant Arabidopsis thaliana. This chapter discusses the principle of VISUAL and how it can be used to investigate phloem differentiation, for example in combination with genetic experiments or transcriptome analysis. In addition, the protocol for establishing a phloem cell culture is provided.

Bimolecular Fluorescence Complementation (BiFC) in Tissue Culture and in Developing Tissues of Drosophila to Study Protein-Protein Interactions

Protein-protein interactions provide a common mechanism for regulating protein functions and also serve as the fundamental step of many biochemical reactions. To accurately determine the involvement and function of protein-protein interactions, it is crucial to detect the interactions with the minimum number of artifacts. In this chapter, we report the method of bimolecular fluorescence complementation (BiFC) in tissue culture and developing tissues of Drosophila, which allows the visualization of subcellular localization of protein-protein interactions in living cells.

Structural, physiological and genetic diversification of Silene vulgaris ecotypes from heavy metal-contaminated areas and their synchronous in vitro cultivation

Results provide significant comparison of leaf anatomy, pigment content, antioxidant response and phenolic profile between individuals from miscellaneous populations and describe unified cultivation protocols for further research on stress biology. The plant communities growing on heavy metal-polluted areas have attracted considerable attention due to their unique ability to tolerate enormous amounts of toxic ions. Three ecotypes of Silene vulgaris representing calamine (CAL), serpentine (SER) and non-metallicolous (NM) populations were evaluated to reveal specific adaptation traits to harsh environment. CAL leaves presented a distinct anatomical pattern compared to leaves of SER and NM plants, pointing to their xeromorphic adaptation. These differences were accompanied by divergent accumulation and composition of photosynthetic pigments as well as antioxidant enzyme activity. In CAL ecotype, the mechanism of reactive oxygen species scavenging is based on the joint action of superoxide dismutase and catalase, but in SER ecotype on superoxide dismutase and guaiacol-type peroxidase. On the contrary, the concentration of phenylpropanoids and flavonols in the ecotypes was unchanged, implying the existence of similar pathways of their synthesis/degradation functioning in CAL and SER populations. The tested specimens showed genetic variation (atpA/MspI marker). Based on diversification of S. vulgaris populations, we focused on the elaboration of similar in vitro conditions for synchronous cultivation of various ecotypes. The most balanced shoot culture growth was obtained on MS medium containing 0.1 mg l^-1 NAA and 0.25 mg l^-1 BA, while the most abundant callogenesis was observed on MS medium enriched with 0.5 mg l^-1 NAA and 5.0 mg l^-1 BA. For the first time, unified in vitro protocols were described for metallophytes providing the opportunity to conduct basic and applied research on stress biology and tolerance mechanisms under freely controlled conditions.

Acquirement of CRY8DB Transgenic Tall Fescue (Festuca arundinacea Schreb.) by Agrobacterium tumefaciens to Develop Resistance Against Pentodon idiota Herbest

Tall fescue plants are widely exposed to white grubs. Regarding the rate of damage caused by the white grubs to tall fescue and difficulty of its ecological and economical control, production of resistant cultivars is a priority. In this experiment, for the first time, we report production of transgenic lines resistant to white grub using CR8DB gene. For this, mature seeds were placed on MS basal medium with 0-15 mg L^-1 2,4-D for callogenesis and 0-1.75 mg L^-1 BA for regeneration. 'Asterix' (54.11%) in 7.5 and 'Talladega' (52.53%) in 10 mg L^-1 2,4-D showed maximum callogenesis. Regeneration percentage was higher in 0.5 mg L^-1 BA. Agrobacterium tumefaciens strain LBA4404 harbouring binary vector pCAMBIA 1301 with CRY8DB gene, which contains HPTII gene and uidA and various types MS media were used for transformation of calli. The highest percentage of gus enzyme activity and hygromycin resistance in calli was related to the modified medium type 11. The PCR and RT-PCR analysis was done to confirm the presence and expression of the target gene in transgenic 5 lines in 'Asterix' and 3 lines in 'Talladega'. According to bioassay, larvae mortality of 91.66% was observed in transgenic plants, whereas it was 15.52% in control plants.

An amended history of tissue culture: Concerning Harrison, Burrows, Mall, and Carrel

The origin of tissue culture is commonly dated to 1907 and credited to Ross Harrison at Hopkins Medical School. But an unpublished letter from the 1942 offers a different interpretation and gives priority to Montrose Burrows with important contributions for the development of cell culture by Franklin Mall at Hopkins and Alexis Carrel at the Rockefeller Institute in New York City. The early development of tissue culture is reviewed and its applications in modern biology and medicine are briefly outlined.

Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration

Current approaches for dynamic profiling of single cells rely on dissociated cultures, which lack important biological features existing in tissues. Organotypic slice cultures preserve aspects of structural and synaptic organisation within the brain and are amenable to microscopy, but established techniques are not well adapted for high throughput or longitudinal single cell analysis. Here we developed a custom-built, automated confocal imaging platform, with improved organotypic slice culture and maintenance. The approach enables fully automated image acquisition and four-dimensional tracking of morphological changes within individual cells in organotypic cultures from rodent and human primary tissues for at least 3 weeks. To validate this system, we analysed neurons expressing a disease-associated version of huntingtin (HTT586Q138-EGFP), and observed that they displayed hallmarks of Huntington's disease and died sooner than controls. By facilitating longitudinal single-cell analyses of neuronal physiology, our system bridges scales necessary to attain statistical power to detect developmental and disease phenotypes.

L-lactate induces specific genome wide alterations of gene expression in cultured bovine granulosa cells

Background

Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate induced transformation. Cultured estrogen producing GC treated either with L-lactate or vehicle control were subjected to mRNA microarray analysis.

Results

The analysis revealed 487 differentially expressed clusters, representing 461 annotated genes. Of these, 333 (= 318 genes) were identified as up- and 154 (= 143 genes) as down-regulated. As the top up-regulated genes we detected TXNIP, H19 and AHSG as well as our previously established marker transcripts RGS2 and PTX3. The top down-regulated genes included VNN1, SLC27A2 and GFRA1, but also MYC and the GC marker transcript CYP19A1. Pathway analysis with differentially expressed genes indicated “cAMP-mediated signaling” and “Axon guidance signaling” among the most affected pathways. Furthermore, estradiol, progesterone and Vegf were identified as potential upstream regulators. An effector network analysis by IPA provided first hints that processes of “angiogenesis” and “vascularization”, but also “cell movement” appeared to be activated, whereas “organismal death” was predicted to be inhibited.

Conclusions

Our data clearly show that L-lactate alters gene expression in cultured bovine GC in a broad, but obviously specific manner. Pathway analysis revealed that the mode of L-lactate action in GC initiates angiogenic processes, but also migratory events like cell movement and axonal guidance signaling, thus supporting the transformation of GC into an early luteal phenotype.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5657-6) contains supplementary material, which is available to authorized users.

Application of genetics and biotechnology for improving medicinal plants

Plant tissue culture has been used for conservation, micropropagation, and in planta overproduction of some pharma molecules of medicinal plants. New biotechnology-based breeding methods such as targeted genome editing methods are able to create custom-designed medicinal plants with different secondary metabolite profiles. For a long time, humans have used medicinal plants for therapeutic purposes and in food and other industries. Classical biotechnology techniques have been exploited in breeding medicinal plants. Now, it is time to apply faster biotechnology-based breeding methods (BBBMs) to these valuable plants. Assessment of the genetic diversity, conservation, proliferation, and overproduction are the main ways by which genetics and biotechnology can help to improve medicinal plants faster. Plant tissue culture (PTC) plays an important role as a platform to apply other BBBMs in medicinal plants. Agrobacterium-mediated gene transformation and artificial polyploidy induction are the main BBBMs that are directly dependent on PTC. Manageable regulation of endogens and/or transferred genes via engineered zinc-finger proteins or transcription activator-like effectors can help targeted manipulation of secondary metabolite pathways in medicinal plants. The next-generation sequencing techniques have great potential to study the genetic diversity of medicinal plants through restriction-site-associated DNA sequencing (RAD-seq) technique and also to identify the genes and enzymes that are involved in the biosynthetic pathway of secondary metabolites through precise transcriptome profiling (RNA-seq). The sequence-specific nucleases of transcription activator-like effector nucleases (TALENs), zinc-finger nucleases, and clustered regularly interspaced short palindromic repeats-associated (Cas) are the genome editing methods that can produce user-designed medicinal plants. These current targeted genome editing methods are able to manage plant synthetic biology and open new gates to medicinal plants to be introduced into appropriate industries.

In vitro growth of Physalis peruviana L. affected by silver nanoparticles

The effect of silver nanoparticles (AgNPs) on plant cells, since their phytotoxicity potential is not yet fully understood. In this context, the aim of the present study was to elucidate the effects of AgNPs in the in vitro culture of Physalis peruviana. For this purpose, P. peruviana seeds were grown in MS medium supplemented with different concentrations of AgNPs. Growth and development of seedlings were evaluated through germination, seedling size and biomass and biochemical and anatomical analyses. At the end of 60 days of cultivation, it was observed that the in vitro germination of this species is not affected by the presence of AgNPs and that at low concentrations (0.385 mg L^-1) it can promote an increase in seedlings biomass. However, higher concentration (15.4 mg L^-1) leads to a reduction in seedling size and root system, but no changes were observed in the seedlings antioxidant metabolism and anatomy. These results demonstrate that the phytotoxicity of AgNPs in P. peruviana is related to the concentration of nanoparticles to which the specie is exposed.

In vitro transplantation of spermatogonial stem cells isolated from human frozen-thawed testis tissue can induce spermatogenesis under 3-dimensional tissue culture conditions

Background

Sperm production is one of the most complex biological processes in the body. In vitro production of sperm is one of the most important goals of researches in the field of male infertility treatment, which is very important in male cancer patients treated with gonadotoxic methods and drugs. In this study, we examine the progression of spermatogenesis after transplantation of spermatogonial stem cells under conditions of testicular tissue culture.

Results

Testicular tissue samples from azoospermic patients were obtained and then these were freeze–thawed. Spermatogonial stem cells were isolated by two enzymatic digestion steps and the identification of these cells was confirmed by detecting the PLZF protein. These cells, after being labeled with DiI, were transplanted in azoospermia adult mice model. The host testes were placed on agarose gel as tissue culture system. After 8 weeks, histomorphometric, immunohistochemical and molecular studies were performed. The results of histomorphometric studies showed that the mean number of spermatogonial cells, spermatocytes and spermatids in the experimental group was significantly more than the control group (without transplantation) (P < 0.05) and most of the cells responded positively to the detection of DiI. Immunohistochemical studies in host testes fragments in the experimental group express the PLZF, SCP3 and ACRBP proteins in spermatogonial cells, spermatocyte and spermatozoa, respectively, which confirmed the human nature of these cells. Also, in molecular studies of PLZF, Tekt1 and TP1, the results indicated that the genes were positive in the test group, while not in the control group.

Conclusion

These results suggest that the slow freezing of SSCs can support the induction of spermatogenesis to produce haploid cells under the 3-dimensional testicular tissue culture.

CoverageTool: A semi-automated graphic software: applications for plant phenotyping

BACKGROUND

Characterization and quantification of visual plant traits is often limited to the use of tools and software that were developed to address a specific context, making them unsuitable for other applications. CoverageTool is flexible multi-purpose software capable of area calculation in cm², as well as coverage area in percentages, suitable for a wide range of applications.

RESULTS

Here we present a novel, semi-automated and robust tool for detailed characterization of visual plant traits. We demonstrate and discuss the application of this tool to quantify a broad spectrum of plant phenotypes/traits such as: tissue culture parameters, ground surface covered by annual plant canopy, root and leaf projected surface area, and leaf senescence area ratio. The CoverageTool software provides easy to use functions to analyze images. While use of CoverageTool involves subjective operator color selections, applying them uniformly to full sets of samples makes it possible to provide quantitative comparison between test subjects.

CONCLUSION

The tool is simple and straightforward, yet suitable for the quantification of biological and environmental effects on a wide variety of visual plant traits. This tool has been very useful in quantifying different plant phenotypes in several recently published studies, and may be useful for many applications.

Metabolic Labeling of Cultured Mammalian Cells for Stable Isotope-Resolved Metabolomics: Practical Aspects of Tissue Culture and Sample Extraction

Stable isotope-resolved metabolomics (SIRM) methods are used increasingly by cancer researchers to probe metabolic pathways and identify vulnerabilities in cancer cells. Analytical and computational advances are being made constantly, but tissue culture and sample extraction procedures are often variable and not elaborated in the literature. This chapter discusses basic aspects of tissue culture practices as they relate to the use of stable isotope tracers and provides a detailed metabolic labeling and metabolite extraction procedure designed to maximize the amount of information that can be obtained from a single tracer experiment.

Genome Editing in Potato with CRISPR/Cas9

Cultivated potato, Solanum tuberosum Group Tuberosum L. (2n = 4x = 48) is a heterozygous tetraploid crop that is clonally propagated, thereby resulting in identical genotypes. Due to the lack of sexual reproduction and its concomitant segregation of alleles, genetic engineering is an efficient way of introducing crop improvement traits in potato. In recent years, genome-editing via the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system for targeted genome modifications has emerged as the most powerful method due to the ease in designing and construction of gene-specific single guide RNA (sgRNA) vectors. These sgRNA vectors are easily reprogrammable to direct Streptococcus pyogenes Cas9 (SpCas9) to generate double stranded breaks (DSBs) in the target genomes that are then repaired by the cell via the error-prone non-homologous end-joining (NHEJ) pathway or by precise homologous recombination (HR) pathway. CRISPR/Cas9 technology has been successfully implemented in potato for targeted mutagenesis to generate knockout mutations (by means of NHEJ) as well as gene targeting to edit an endogenous gene (by HR). In this chapter, we describe procedures for designing sgRNAs, protocols to clone sgRNAs for CRISPR/Cas9 constructs to generate knockouts, design of donor repair templates and use geminivirus replicons (GVRs) to facilitate gene-editing by HR in potato. We also describe tissue culture procedures in potato for Agrobacterium-mediated transformation to generate gene-edited events along with their molecular characterization.