Development of a nine-variant reference material panel to standardize cell-free DNA detection

Detection of specific gene mutations in cell-free DNA (cfDNA) serves as a valuable cancer biomarker and is increasingly being explored as an appealing alternative to tissue-based methods. However, the lack of available reference materials poses challenges in accurately evaluating the performance of different assays. In this study, we present the development of a comprehensive reference material panel for cfDNA detection, encompassing nine hotspot mutations in KRAS/BRAF/EGFR/PIK3CA at three variant allele frequencies (VAFs), ranging from 0.33 to 23.9%. To mimic cfDNA, these reference materials were generated by enzymatically digesting cell-line DNA into approximately 154-bp to 173-bp fragments using a laboratory-developed reaction system. The VAFs for each variation were precisely determined through validated digital PCR assays with high accuracy. Furthermore, the reliability and applicability of this panel were confirmed through two independent NGS assays, yielding concordant results. Collectively, our findings suggest that this novel reference material panel holds great potential for validation, evaluation, and quality control processes associated with liquid biopsy assays.

Identification and annotation of milk associated genes from milk somatic cells using expression and RNA-seq data

It is of interest to identify and annotate milk associated genes using expression profiling and RNA-Seq data from milk somatic cells. RNA-Seq data was pre-processed and mapping was done to identify differentially expressed genes (DEG). The functional insights about the up and down regulated genes were gleaned using the protein-protein interaction Network in the STRING database followed by CytoHubba analysis in Cytoscope. Gene ontology, annotation and pathway enrichment was completed using ShinyGO, David tool and QTL analysis. These analysis shows that 21 genes are linked with the secretion of milk.

Spectroscopic and microscopic comparisons of cell topology and chemistry analysis of mouse embryonic stem cell, somatic cell and cancer cell

While embryonic stem cells and cancer cells are known to have many similarities in signalling pathways, healthy somatic cells are known to be different in many ways. Characterization of embryonic stem cell is crucial for cancer development and cancer recurrence due to the shared signalling pathways and life course with cancer initiator and cancer stem cells. Since embryonic stem cells are the sources of the somatic and cancer cells, it is necessary to reveal the relevance between them. The past decade has seen the importance of interdisciplinary studies and it is obvious that the reflection of the physical/chemical phenomena occurring on the cell biology has attracted much more attention. For this reason, the aim of this study is to elementally and topologically characterize the mouse embryonic stem cells, mouse lung squamous cancer cells, and mouse skin fibroblast cells by using Atomic Force Microscopy (AFM), X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM) supported with Electron Dispersive Spectroscopy (EDS) techniques in a complementary way. Our AFM findings revealed that roughness data of the mouse embryonic stem cells and cancer cells were similar and somatic cells were found to be statistically different from these two cell types. However, based on both XPS and SEM-EDS results, surface elemental ratios vary in mouse embryonic stem cells, cancer cells and somatic cells. Our results showed that these complementary spectroscopic and microscopic techniques used in this work are very effective in cancer and stem cell characterization and have the potential to gather more detailed information on relevant biological samples.

Herd-level contamination of Neospora caninum, Toxoplasma gondii and Brucella in milk of Iranian dairy farms

The bulk milk examination is a reliable screening tool for monitoring the quality of milk in the farms. The infection to Neospora caninum, Toxoplasma gondii and Brucella sp. Was evaluated in bulk milk samples of dairy farms in Hamedan province, West part of Iran. All the dairy farms (n = 149) were examined for N. caninum, T. gondii and Brucella infections using milk ring test (MRT), microbiology, serology (Enzyme-linked Immunosorbent Assay), and molecular techniques. Based on molecular methods, Brucella-infection was negative in all farms; while, 55 %, 5.4 % and 2.7 % of samples were positive for N. caninum, T. gondii and mix infection, respectively. The highest Neospora-infection was detected in the farms with history of abortion in fall and winter. There was significant association between Neospora-infection and the presence of dogs and rodents in the farms, herd size, and age of the animals. Also, a significant association was seen between Toxoplasma-infection and the presence of cats and rodents in the farms, as well as age of the animals. Average total bacterial count (TBC) was calculated 1.14 × 10⁶±1.1 × 10⁶. The highest TBC was in the farms from Central locations of studied area (5.7 × 10⁶±2.24 × 10⁶), farms with more than 120 animals (7.9 × 10⁶±2.8 × 10⁶), and farms with ≥50-months age (1.74 × 10⁶±6.3 × 10⁵) in spring and summer (6.9 × 10⁶±3.7 × 10⁶). The number of somatic cells was estimated between 1 × 10⁴ and 2 × 10⁶ (Average = 4.2 × 10⁵±3.39 × 10⁵). The current study was a comprehensive evaluation of Neospora, Toxoplasma and Brucella infections in milk samples of Iranian dairy farms for the first time. Neospora-infection is responsible for economic losses in the region. Health education and milk pasteurization are so helpful for inhibiting the milk borne diseases. To reduce the risk factors, predict and design the appropriate schemes like redundant of heterogeneous animals are recommended.

Amh dominant expression in Sertoli cells during the testicular differentiation and development stages in the olive flounder Paralichthys olivaceus

The olive flounder Paralichthys olivaceus, an important marine fish, shows gender differences in growth. The mechanism on its gonadal differentiation direction affected with exogenous factors still needs to be clarified. The anti-Müllerian hormone (amh) gene is involved in fish testicular differentiation and maintenance. The aim of this study was to investigate the expression of the flounder amh in tissues and the gonads. The quantitative expression analysis results showed that it was highly expressed in the testis, especially in the testis at stages I - IV (P < 0.05). Also, amh was detected in Sertoli cells surrounding spermatogonia and peripheral seminiferous lobule of the testis with in situ hybridization (ISH) and immunohistochemistry (IHC). During the differentiation period, the amh expression in the testis of the tamoxifen treatment group (100 ppm) was higher than that in the ovary of the 17β-estradiol (E2, 5 ppm) group, and the expression levels of amh during process of the male differentiation in the tamoxifen group were higher than those in the 17ɑ-methyltestosterone (MT, 5 ppm) group (P < 0.05). ISH results also exhibited that amh was expressed in the somatic cells that surrounded the germ cells of juvenile flounder similar to adult ones. Furthermore, the flounder gonads in the tamoxifen group maintained more germ cells and somatic cells than those in the MT group from 20 to 80 mm total length (TL). Especially, at 60 and 80 mm TL, the numbers of germ and somatic cells in the tamoxifen group were significantly higher than those in the MT group (P < 0.05). In summary, amh might initiate the process of testicular differentiation, and is involved in the early development and maintenance of testis.

The proliferative lifespan of adult sheep fibroblasts can be conditionally extended by tetracycline-inducible expression of human telomerase reverse transcriptase

Forced expression of human telomerase reverse transcriptase (hTERT) has been used to immortalize mammalian cells. Here, we report conditional extension of proliferative lifespan of adult sheep somatic cells by introducing tetracycline-inducible (Tet-on) expression of hTERT. After transfecting adult sheep fibroblasts with the vector for Tet-on induced conditional expression of hTERT, we obtained several hTERT-positive clones that exhibited extended-lifespan under the induction of tetracycline analogue, doxycycline. Further assays for a representative cell clone A3h38 indicated that the cells had a much stronger proliferative ability than control primary cells, as assessed by population doubling levels and single-cell cloning efficiency. A3h38 cells could maintain vigorous growth in culture for more than 150 days but they became senescent when hTERT expression was abrogated by withdrawal of doxycycline. Although having undergone long-term culture, the nuclei of A3h38 cells could support higher preimplantation development of somatic cell nuclear transfer embryos than control primary cells. These results demonstrated that conditional expression of hTERT could reversibly extend the lifespan of adult sheep fibroblasts, enhance their proliferation and maintain their ability to be reprogrammed after nuclear transfer. This strategy would also be applicable to many other somatic cell types in more species.

Concise Review: Heart-Derived Cell Therapy 2.0: Paracrine Strategies to Increase Therapeutic Repair of Injured Myocardium

Despite progress in cardiovascular medicine, the incidence of heart failure is rising and represents a growing challenge. To address this, ex vivo proliferated heart-derived cell products have emerged as a promising investigational cell-treatment option. Despite being originally proposed as a straightforward myocyte replacement strategy, emerging evidence has shown that cell-mediated gains in cardiac function are leveraged on paracrine stimulation of endogenous repair and tissue salvage. In this concise review, we focus on the paracrine repertoire of heart-derived cells and outline strategies used to boost cell potency by targeting cytokines, metabolic preconditioning and supportive biomaterials. Mechanistic insights from these studies will shape future efforts to use defined factors and/or synthetic cell approaches to help the millions of patients worldwide suffering from heart failure. Stem Cells 2018;36:1794-10.

Subclinical mastitis interferes with ovulation, oocyte and granulosa cell quality in dairy cows

The objective was to evaluate the effect of mastitis by somatic cell count (SCC) on follicular growth, ovulation, oocytes and cumulus cells quality and on the concentration and size of exosomes in follicular fluid of dairy cows. In the study, crossbred cows (Bos taurus - Holstein x Bos indicus - Gir) were classified for analysis as Control (SCC<200.000 cells/mL) and Mastitis (SCC>400.000 cells/mL) groups. In experiment 1 (follicular dynamics), cows (n = 57) were submitted to ultrasound evaluations every 24 h, from progesterone-releasing-intravaginal-device (PRID) removal (D8) until 48 h later (D10). Thereafter, evaluations were performed every 12 h, until ovulation or up to 96 h after PRID removal. In experiment 2 (oocyte, cumulus complexes, and follicular fluid evaluation), cows (n = 26) were submitted to follicular aspiration (OPU) for oocyte quality and cumulus cells transcript evaluation. The amount of cumulus complexes transcripts (BCL2, BAX, PI3K, PTEN, FOXO3) was determined by Real-Time Polymerase Chain Reaction. Moreover, seven days after the OPU session, the dominant follicle was aspirated. Exosomes were isolated from the follicular fluid for evaluation of particle size and concentration. Ovulation rate [Control 77.4% (24/31) and Mastitis 57.7% (15/26); P = 0.09] and viable oocytes rate [Control 59.1% (130/220) and Mastitis 41.9% (125/298); P = 0.01] were higher in Control animals. Additionally, there was a greater number of degenerate oocytes [Control 6.7 ± 1.2 and Mastitis 13.3 ± 5.5; (P = 0.001)] in subclinical mastitis cows. There was greater abundance (P = 0.003) of BAX cumulus cell transcripts and exosome mean (P = 0.03) and mode (P = 0.02) was smaller in subclinical mastitis cows. In conclusion, ovulation rate, oocyte quality, and exosome diameter were smaller in cows with SCC>400.000 cells/mL.

Conservation of somatic tissue derived from collared peccaries (Pecari tajacu Linnaeus, 1758) using direct or solid-surface vitrification techniques

Cryopreservation of somatic tissue can be applied in biodiversity conservation, especially for wild species as collared peccary. We aimed to evaluate the effect of vitrification techniques of ear tissue of collared peccary [direct vitrification in cryovials (DVC) or solid-surface vitrification (SSV)] on the layers of epidermis and dermis by conventional histology and cell ability during the in vitro culture. Thus, both the vitrification methods were able to maintain normal patterns of the epidermis as the cornea and granular layers, furthermore the intercellular space and dermal-epidermal junction of the spinous layer when compared to fresh control. Nevertheless, DVC and SSV percentage of normality decreased in the morphological integrity of cytoplasm (37.5 and 25.0%) of spinous layer, respectively, as compared to the fresh fragments (100%, p < 0.05). Moreover, other differences between the fresh control (100%) and DVC tissues were verified in the intra-epidermal cleavage of the spinous (37.5%) and basal (37.5%) layers. In general, DVC and SSV techniques were efficient for the recovery of the somatic cells according to most of the evaluated parameters for the in vitro culture (p > 0.05). In addition, only at time of 72 h (D3), in the growth curve, DVC fragments showed a reduced cell concentration than fresh control. In conclusion, SSV was found to be a more efficient method for vitrifying collared peccary skin tissue when compared to DVC. These results are relevant for the tissue cryopreservation from collared peccary and could also be useful for mammals with phylogenetic relationships.

Rediscovery of the species of 'ancestral Volvox': morphology and phylogenetic position of Pleodorina sphaerica (Volvocales, Chlorophyceae) from Thailand

Pleodorina sphaerica Iyengar was considered to be a phylogenetic link between Volvox and the type species Pleodorina californica Shaw because it has small somatic cells distributed from the anterior to posterior poles in 64- or 128-celled vegetative colonies. However, cultural studies and molecular and ultrastructural data are lacking in P. sphaerica, and this species has not been recorded since 1951. Here, we performed light and electron microscopy and molecular phylogeny of P. sphaerica based on newly established culture strains originating from Thailand. Morphological features of the present Thai species agreed well with those of the previous studies of the Indian material of P. sphaerica and with those of the current concept of the advanced members of the Volvocaceae. The present P. sphaerica strains exhibited homothallic sexuality; male and facultative female colonies developed within a single clonal culture. Chloroplast multigene phylogeny demonstrated that P. sphaerica was sister to two other species of Pleodorina (P. californica and Pleodorina japonica Nozaki) without posterior somatic cells, and these three species of Pleodorina formed a robust clade, which was positioned distally in the large monophyletic group including nine taxa of Volvox sect. Merrillosphaera and Volvox (sect. Janetosphaera) aureus Ehrenberg. Based on the present phylogenetic results, evolutionary losses of posterior somatic cells might have occurred in the ancestor of P. californica and P. japonica. Thus, P. sphaerica might represent an ancestral morphology of Pleodorina, rather than of Volvox.

nr0b1 (DAX1) mutation in zebrafish causes female-to-male sex reversal through abnormal gonadal proliferation and differentiation

Sex determinations are diverse in vertebrates. Although many sex-determining genes and pathways are conserved, the mechanistic roles of these genes and pathways in the genetic sex determination are not well understood. DAX1 (encoded by the NR0B1 gene) is a vertebrate specific orphan nuclear receptor that regulates gonadal development and sexual determination. In human, duplication of the NR0B1 gene leads to male-to-female sex reversal. In mice, Nr0b1 shows both pro-testis and anti-testis functions. We generated inheritable nr0b1 mutation in the zebrafish and found the nr0b1 mutation caused homozygous mutants to develop as fertile males due to female-to-male sex reversal. The nr0b1 mutation did not increase Caspase-3 labeling nor tp53 expression in the developing gonads. Introduction of a tp53 mutation into the nr0b1 mutant did not rescue the sex-reversal phenotype. Further examination revealed reduction in cell proliferation and abnormal somatic cell differentiation in the nr0b1 mutant gonads at the undifferentiated and bi-potential ovary stages. Together, our results suggest nr0b1 regulates somatic cell differentiation and cell proliferation to ensure normal sex development in the zebrafish.

Somatic cell reprogramming-free generation of genetically modified pigs

Genetically modified pigs for biomedical applications have been mainly generated using the somatic cell nuclear transfer technique; however, this approach requires complex micromanipulation techniques and sometimes increases the risks of both prenatal and postnatal death by faulty epigenetic reprogramming of a donor somatic cell nucleus. As a result, the production of genetically modified pigs has not been widely applied. We provide a simple method for CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 gene editing in pigs that involves the introduction of Cas9 protein and single-guide RNA into in vitro fertilized zygotes by electroporation. The use of gene editing by electroporation of Cas9 protein (GEEP) resulted in highly efficient targeted gene disruption and was validated by the efficient production of Myostatin mutant pigs. Because GEEP does not require the complex methods associated with micromanipulation for somatic reprogramming, it has the potential for facilitating the genetic modification of pigs.