Lymphoid lineage differentiation potential of mouse nuclear transfer embryonic stem cells.

Stem cells therapy is considered as an efficient strategy for the treatment of some diseases. Nevertheless, some obstacles such as probability of rejection by the immune system limit applications of this strategy. Therefore, several efforts have been made to overcome this among which using the induced pluripotent stem cells (iPSCs) and nuclear transfer embryonic stem cell (nt-ESCs) are the most efficient strategies. The objective of this study was to evaluate the differentiation potential of the nt-ESCs to lymphoid lineage in the presence of IL-7, IL-3, FLT3-ligand and TPO growth factors in vitro. To this end, the nt-ESCs cells were prepared and treated with aforementioned growth factors for 7 and 14 days. Then, the cells were examined for expression of lymphoid markers (CD3, CD25, CD127 and CD19) by quantitative PCR (q-PCR) and flow cytometry. An increased expression of CD19 and CD25 markers was observed in the treated cells compared with the negative control samples by day 7. After 14 days, the expression level of all the tested CD markers significantly increased in the treated groups in comparison with the control. The current study reveals the potential of the nt-ESCs in differentiation to lymphoid lineage in the presence of defined growth factors.

Looking for the sponge loop: analyses of detritus on a Caribbean forereef using stable isotope and eDNA metabarcoding techniques.

Coral reefs are biodiverse ecosystems that rely on trophodynamic transfers from primary producers to consumers through the detrital pathway. The sponge loop hypothesis proposes that sponges consume dissolved organic carbon (DOC) and produce large quantities of detritus on coral reefs, with this turn-over approaching the daily gross primary production of the reef ecosystem. In this study, we collected samples of detritus in the epilithic algal matrix (EAM) and samples from potential sources of detritus over two seasons from the forereef at Carrie Bow Cay, Belize. We chose this location to maximize the likelihood of finding support for the sponge loop hypothesis because Caribbean reefs have higher sponge abundances than other tropical reefs worldwide and the Mesoamerican barrier reef is an archetypal coral reef ecosystem. We used stable isotope analyses and eDNA metabarcoding to determine the composition of the detritus. We determined that the EAM detritus was derived from a variety of benthic and pelagic sources, with primary producers (micro- and macroalgae) as major contributors and metazoans (Arthropoda, Porifera, Cnidaria, Mollusca) as minor contributors. None of the sponge species that reportedly produce detritus were present in EAM detritus. The cnidarian signature in EAM detritus was dominated by octocorals, with a scarcity of hard corals. The composition of detritus also varied seasonally. The negligible contribution of sponges to reef detritus contrasts with the detrital pathway originally proposed in the sponge loop hypothesis. The findings indicate a mix of pelagic and benthic sources in the calmer summer and primarily benthic sources in the more turbulent spring.

Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence-based metabarcoding.

Environmental DNA (eDNA)-based methods of species detection are enabling various applications in ecology and conservation including large-scale biomonitoring efforts. qPCR is widely used as the standard approach for species-specific detection, often targeting a fish species of interest from aquatic eDNA. However, DNA metabarcoding has the potential to displace qPCR in certain eDNA applications. In this study, we compare the sensitivity of the latest Illumina NovaSeq 6000 NGS platform to qPCR TaqMan assays by measuring limits of detection and by analysing eDNA from water samples collected from Churchill River and Lake Melville, NL, Canada. Species-specific, targeted next generation sequencing (NGS) assays had significantly higher sensitivity than qPCR, with limits of detection 14- to 29-fold lower. For example, when analysing eDNA, qPCR detected Gadus ogac (Greenland cod) in 21% of samples, but targeted NGS detected this species in 29% of samples. General NGS assays were as sensitive as qPCR, while simultaneously detecting 15 fish species from eDNA samples. With over 34,000 fish species on the planet, parallel and sensitive methods such as NGS will be required to support effective biomonitoring at both regional and global scales.

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes.

The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification, and are capable of simultaneously providing valuable information on other taxonomic groups.

The genetic architecture of Stargardt macular dystrophy (STGD1): a longitudinal 40-year study in a genetic isolate.

Stargardt disease (STGD1) is a form of inherited retinal dystrophy attributed to variants affecting function of the large ABCA4 gene and is arguably the most complex monogenic disease. Therapeutic trials in patients depend on identifying causal ABCA4 variants in trans, which is complicated by extreme allelic and clinical heterogeneity. We report the genetic architecture of STGD1 in the young genetically isolated population of Newfoundland, Canada. Population-based clinical recruitment over several decades yielded 29 STGD1 and STGD1-like families (15 multiplex, 14 singleton). Family interviews and public archival records reveal the vast majority of pedigree founders to be of English extraction. Full gene sequencing and haplotype analysis yielded a high solve rate (38/41 cases; 92.7%) for STGD1 and identified 16 causative STGD1 alleles, including a novel deletion (NM_000350.3: ABCA4 c.67-1delG). Several STGD1 alleles of European origin (including NM_000350.3: ABCA4 c.5714 + 5G>A and NM_000350.3: ABCA4 c.5461-10T>C) have drifted to a relatively high population frequency due to founder effect. We report on retinal disease progression in homozygous patients, providing valuable allele-specific insights. The least involved retinal disease is seen in patients homozygous for c.5714 + 5G>A variant, a so-called "mild" variant which is sufficient to precipitate a STGD1 phenotype in the absence of other pathogenic variants in the coding region and intron/exon boundaries of ABCA4. The most severe retinal disease is observed in cases with ABCA4 c.[5461-10T>C;5603A>T] complex allele. We discuss the advantages of determining genetic architecture in genetic isolates in order to begin to meet the grand challenge of human genetics.

Melatonin Improves The Developmental Competence of Goat Oocytes.

BACKGROUND: DNA methylation is one the epigenetic mechanisms, which is critically involved in gene expression. This phenomenon is mediated by DNA methyl-transferases and is affected by environmental stress, including in vitro maturation (IVM) of oocytes. Melatonin, as an antioxidant, may theoretically be involved in epigenetic regulation via reductions of reactive oxygen species. This study was performed to investigate DNA methylation and the possibility of goat oocyte development after treatment with different concentrations of melatonin. MATERIALS AND METHODS: This experimental study was performed to investigate DNA methylation and the possibility of goat oocyte development after treatment with different concentrations of melatonin. For this purpose, oocytes with granulated cytoplasm were selected and co-cultured with at least two layers of cumulus cells in maturation medium with 10-6 M, 10-9 M, 10-12 M and 0-M (as control group) of melatonin. Nucleus status, glutathione content and developmental competence of the oocytes in each experimental group were assessed. Also, expression of genes associated with DNA methylation, including DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3b (DNMT3b) and DNA methyltransferase 3a (DNMT3a) was evaluated by quantitative real time-polymerase chain reaction (RT-PCR). RESULTS: According to our findings, the percentage of oocytes that reached the M-II stage significantly increased in the 10-12 M group (P<0.05). Also, a significant elevation of glutathione content was observed in melatonin-treated oocytes (P<0.05). Analysis of blastocyst formation revealed that developmental competence of the oocytes was higher than the control group (P<0.05). It was observed that melatonin treatment decreased expression levels of DNA methyltransferases (DNMTs) and global DNA methylation (P<0.05). In addition, the expression of melatonin receptor1A (MTNR1A) was detected in both cumulus and oocyte by RT-PCR. CONCLUSION: The results suggested that in goat model melatonin affects DNA methylation pattern, leading to an improvement in the developmental competence of the oocytes.

The influence of semen quality on male pronucleus demethylation process during ICSI cycle.

There is growing evidence that the spermatozoon's epigenetic structure is of the utmost importance in the health of the future embryo. Following fertilization, sperm chromatin undergoes epigenetic reprogramming including DNA demethylation and remethylation, which resets gene expression. In some infertile patients, it is inevitable that sperm cells that are not within the range of normal human sperm parameters will be used for intracytoplasmic sperm injection. Understanding the relationship between the human sperm parameters and male pronucleus DNA demethylation seems necessary. We hypothesized that demethylation of the male pronucleus might be altered in zygotes conceived from a spermatozoa obtained from a sample exhibiting an abnormal semen analysis profile. To test the hypothesis, sperm cells from normal and abnormal human semen samples were injected into mouse oocytes. A group of cultured zygotes was fixed before the onset of DNA demethylation and the other group was fixed after DNA demethylation. Both groups were then labeled with a 5 methylcytosine antibody and the level of pronuclei methylation was detected as a function of fluorescent intensity. The level of demethylation was then determined as the difference between 5 methylcytosine fluorescent intensity before and after DNA demethylation. A negative correlation (p<0.05) was observed between sperm motility, morphology, percentage of head defects, protamine deficiency, and DNA demethylation level. However, no correlation was found between the demethylation level and sperm count. In conclusion, these observations suggest that demethylation is altered in the male pronucleus when low quality sperm samples are used.

Pronuclear epigenetic modification of protamine deficient human sperm following injection into mouse oocytes.

Epigenetic abnormalities and abnormal chromatin structure in sperm may lead to male infertility. Protamine deficiency is among the disorders of chromatin structure in sperm. The study of epigenetic changes in male pronuclei is necessary since abnormal sperm is sometimes used to create embryos using assisted reproductive techniques. The present study was carried out to compare epigenetic global marks in male pronuclei derived from normal and protamine deficient sperm cells. To do so, interspecies fertilization was used to obtain the male pronucleus. Normal and protamine deficient sperm cells, which were identified by chromomycin A3 staining, were injected into mouse oocytes. Oocytes were cultured until pronuclear formation and were then labeled with different antibodies (anti 5-methylcytosine, anti 5-hydroxymethylcytosine, and anti acetyl H4K12). Based on the fluorescence intensity, the level of each of these epigenetic factors was determined and they revealed a significant relationship between the level of sperm protamine deficiency and sperm epigenetic factors. Protamine deficiency was found to be associated with an increased methylation (p=0) and decreased hydroxymethylation rate (p=0.015) of the male pronucleus chromatin. However, no association was found between protamine deficiency and the level of H4K12 acetylation (p=0.548). Also, the efficiency of fertilization in protamine deficient sperm cells was less than normal. These results suggest that protamine deficient sperm cells lead to the formation of epigenetically altered pronuclei.