Epigenetic dynamics during capacitation of naïve human pluripotent stem cells

Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine. Naïve hPSCs hold promise to overcome some of the limitations of conventional (primed) hPSCs, including recurrent epigenetic anomalies. Naïve-to-primed transition (capacitation) follows transcriptional dynamics of human embryonic epiblast and is necessary for somatic differentiation from naïve hPSCs. We found that capacitated hPSCs are transcriptionally closer to postimplantation epiblast than conventional hPSCs. This prompted us to comprehensively study epigenetic and related transcriptional changes during capacitation. Our results show that CpG islands, gene regulatory elements, and retrotransposons are hotspots of epigenetic dynamics during capacitation and indicate possible distinct roles of specific epigenetic modifications in gene expression control between naïve and primed hPSCs. Unexpectedly, PRC2 activity appeared to be dispensable for the capacitation. We find that capacitated hPSCs acquire an epigenetic state similar to conventional hPSCs. Significantly, however, the X chromosome erosion frequently observed in conventional female hPSCs is reversed by resetting and subsequent capacitation

Rapid assembly of customized TALENs into multiple

Transcriptional activator-like effector nucleases (TALENs) have become a powerful tool for genome editing. Here we present an efficient TALEN assembly approach in which TALENs are assembled by direct Golden Gate ligation into Gateway® Entry vectors from a repeat variable di-residue (RVD) plasmid array. We constructed TALEN pairs targeted to mouse Ddx3 subfamily genes, and demonstrated that our modified TALEN assembly approach efficiently generates accurate TALEN moieties that effectively introduce mutations into target genes. We generated "user friendly" TALEN Entry vectors containing TALEN expression cassettes with fluorescent reporter genes that can be efficiently transferred via Gateway (LR) recombination into different delivery systems. We demonstrated that the TALEN Entry vectors can be easily transferred to an adenoviral delivery system to expand application to cells that are difficult to transfect. Since TALENs work in pairs, we also generated a TALEN Entry vector set that combines a TALEN pair into one PiggyBac transposon-based destination vector. The approach described here can also be modified for construction of TALE transcriptional activators, repressors or other functional domains. © 2013 Zhang et al

The Iranian education and academic mobility model

The paper discusses the evolution of the educational model and trends of academic mobility in the Islamic Republic of Iran (IRI). It analyzes the socio-demographic structure of the population, the dynamics of the number of young people, as well as the dynamics and composition of the country’s school in the country. There is also an examination of the ways in which the process of emigration from Iran had evolved in the context of the country’s socio-political history of the state in the 20th-21st centuries. Various levels of the Iranian education system are considered. The author examines the internationalization trends in higher education. The forms and trends of academic mobility, including exit and entry mobility, are delineated. In recent years, the visiting academic mobility of Iranian students has been targeted at the U.S., Turkey, Italy, Canada, and the UAE. There is a contemplation of the methods used for selecting Iranian students for studying abroad at the state budget’s expense, which is based on a system of state quotas and fairly high requirements for applicants. Iranian students studying abroad receive an academic scholarship. Those who receive such a scholarship must pay a deposit before being issued a final permit, and commit to returning to Iran after graduation and working for up to six years. Recently, increasing the number of foreign students in Iran has become one of the priorities of the Ministry of Science, Research and Technology. The admission of foreign students has presently become one of the most important tasks undertaken by universities. One way to attract more foreign students and compete for them is to raise the status of universities and the country. Iran is growing more attractive as a recipient of international students from certain neighboring countries (Afghanistan, Iraq, Syria, Lebanon, Pakistan, and China). The role of academic mobility in the integration of Iran into the international educational and scientific space and the contribution of academic exchanges to the development of the national culture of Iran are emphasized. © 2019, CA and C Press AB. All rights reserved

Perceptions and attitudes to understand human-wildlife conflict in an urban landscape – A systematic review

Managing human-wildlife conflicts (HWC) in human-dominated habitats is an important issue in wildlife conservation. Understanding and addressing local people’s attitudes and behaviours toward HWC is thought to be imperative for successful human-wildlife co-existence. Despite substantial research and conservation resources being invested to study, protect, and manage HWC globally, research on human perceptions of wildlife is mostly done in silos. Realising the lack of scholarly investigations that focus on such conflicts in urban areas by including perceptions of urban residents, we have made the first step, through a systematic review, to identify progress, gaps and future directions of urban wildlife conflict research. Reviewing all studies published globally (n = 124), we identified nuisance urban wildlife and associated conflicts reported by human residents. The findings revealed that most studies, largely focusing on mammals, were conducted in North America. Based on diet, among the 165 trophic groups studied, the majority were omnivores (n = 67), closely followed by carnivores (n = 50) and herbivores (n = 40). Within vertebrate taxa, bear species (brown, black and sloth bear; Ursus spp., Melursus ursinus) were the most conflictual followed by grey wolf (Canis lupus) and coyote (Canis latrans). The lack of longitudinal research to understand the trends and shifts in urban wildlife population and changes in human perception and attitudes was a key finding. Therefore, if research is not supplemented by long-term follow-up studies, the resolution of HWC in urban areas will be under evaluated. Furthermore, researchers should consider integrating quantitative and qualitative research methods, such as in-depth or focus group interviews, to understand motivations or perceptions to present a holistic picture for urban wildlife conservation. Perceptions may shift over time, and the human dimension of wildlife may serve as an ecological indicator of ecosystem status, providing valuable insight into how management measures will be accepted by citizens, which is critical for their success

Profiling of naïve and primed human pluripotent stem cells reveals state-associated miRNAs

Naïve human pluripotent stem cells (hPSC) resemble the embryonic epiblast at an earlier time-point in development than conventional, ‘primed’ hPSC. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process recapitulating aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly expressed in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in naïve mouse PSC. This aligns with the consensus that naïve hPSC resemble mouse naive PSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference

Transposon mediated BAC transgenesis via pronuclear injection of mouse zygotes.

Pronuclear microinjection of bacterial artificial chromosomes (BACs) is the preferred way to generate transgenic mice because the transgene accurately recapitulates expression of the endogenous gene. However, the method is demanding and the integrity and copy number of the BAC transgene is difficult to control. Here, we describe a simpler pronuclear injection method that relies on transposition to introduce full-length BACs into the mouse genome. The bacterial backbone of a hPAX6-GFP reporter BAC was retrofitted with PiggyBac transposon inverted terminal repeats and co-injected with PiggyBac transposase mRNA. Both the frequency of transgenic founders as well as intact, full-length, single copy integrations were increased. Transposition was determined by a rapid PCR screen for a transpositional signature and confirmation by splinkerette sequencing to show that theBACs were integrated as a single copy either in one or two different genomic sites. BAC transposons displayed improved functional accuracy over random integrants as evaluated by expression of the hPAX6-GFP reporter in embryonic neural tube and absence of ectopic expression. This method involves less work to achieve increased frequencies of both transgenesis and single copy, full-length integrations. These advantages are not only relevant to rodents but also for transgenesis in all systems. genesis 51:135-141, 2013. © 2012 Wiley Periodicals, Inc

Targeted isolation of cloned genomic regions by recombineering for haplotype phasing and isogenic targeting.

Studying genetic variations in the human genome is important for understanding phenotypes and complex traits, including rare personal variations and their associations with disease. The interpretation of polymorphisms requires reliable methods to isolate natural genetic variations, including combinations of variations, in a format suitable for downstream analysis. Here, we describe a strategy for targeted isolation of large regions (∼35 kb) from human genomes that is also applicable to any genome of interest. The method relies on recombineering to fish out target fosmid clones from pools and thereby circumvents the laborious need to plate and screen thousands of individual clones. To optimize the method, a new highly recombineering-efficient bacterial host, including inducible TrfA for fosmid copy number amplification, was developed. Various regions were isolated from human embryonic stem cell lines and a personal genome, including highly repetitive and duplicated ones. The maternal and paternal alleles at the MECP2/IRAK 1 loci were distinguished based on identification of novel allele-specific single-nucleotide polymorphisms in regulatory regions. Additionally, we applied further recombineering to construct isogenic targeting vectors for patient-specific applications. These methods will facilitate work to understand the linkage between personal variations and disease propensity, as well as possibilities for personal genome surgery