Transcript profiling during preimplantation mouse development

AbstractStudies using low-resolution methods to assess gene expression during preimplantation mouse development indicate that changes in gene expression either precede or occur concomitantly with the major morphological transitions, that is, conversion of the oocyte to totipotent 2-cell blastomeres, compaction, and blastocyst formation. Using microarrays, we characterized global changes in gene expression and used Expression Analysis Systematic Explorer (EASE) to identify biological and molecular processes that accompany and likely underlie these transitions. The analysis confirmed previously described processes or events, but more important, EASE revealed new insights. Response to DNA damage and DNA repair genes are overrepresented in the oocyte compared to 1-cell through blastocyst stages and may reflect the oocyte's response to selective pressures to insure genomic integrity; fertilization results in changes in the transcript profile in the 1-cell embryo that are far greater than previously recognized; and genome activation during 2-cell stage may not be as global and promiscuous as previously proposed, but rather far more selective, with genes involved in transcription and RNA processing being preferentially expressed. These results validate this hypothesis-generating approach by identifying genes involved in critical biological processes that can be the subject of a more traditional hypothesis-driven approach

Publishing SNP Genotypes of Human Embryonic Stem Cell Lines: Policy Statement of the International Stem Cell Forum Ethics Working Party

Novel methods and associated tools permitting individual identification in publicly accessible SNP databases have become a debatable issue. There is growing concern that current technical and ethical safeguards to protect the identities of donors could be insufficient. In the context of human embryonic stem cell research, there are no studies focusing on the probability that an hESC line donor could be identified by analyzing published SNP profiles and associated genotypic and phenotypic information. We present the International Stem Cell Forum (ISCF) Ethics Working Party’s Policy Statement on “Publishing SNP Genotypes of Human Embryonic Stem Cell Lines (hESC)”. The Statement prospectively addresses issues surrounding the publication of genotypic data and associated annotations of hESC lines in open access databases. It proposes a balanced approach between the goals of open science and data sharing with the respect for fundamental bioethical principles (autonomy, privacy, beneficence, justice and research merit and integrity)

Rapid screening for chromosomal aneuploidies using array-MLPA

<p>Abstract</p> <p>Background</p> <p>Chromosome abnormalities, especially trisomy of chromosome 21, 13, or 18 as well as sex chromosome aneuploidy, are a well-established cause of pregnancy loss. Cultured cell karyotype analysis and FISH have been considered reliable detectors of fetal abnormality. However, results are usually not available for 3-4 days or more. Multiplex ligation-dependent probe amplification (MLPA) has emerged as an alternative rapid technique for detection of chromosome aneuploidies. However, conventional MLPA does not allow for relative quantification of more than 50 different target sequences in one reaction and does not detect mosaic trisomy. A multiplexed MLPA with more sensitive detection would be useful for fetal genetic screening.</p> <p>Methods</p> <p>We developed a method of array-based MLPA to rapidly screen for common aneuploidies. We designed 116 universal tag-probes covering chromosomes 13, 18, 21, X, and Y, and 8 control autosomal genes. We performed MLPA and hybridized the products on a 4-well flow-through microarray system. We determined chromosome copy numbers by analyzing the relative signals of the chromosome-specific probes.</p> <p>Results</p> <p>In a blind study of 161 peripheral blood and 12 amniotic fluid samples previously karyotyped, 169 of 173 (97.7%) including all the amniotic fluid samples were correctly identified by array-MLPA. Furthermore, we detected two chromosome X monosomy mosaic cases in which the mosaism rates estimated by array-MLPA were basically consistent with the results from karyotyping. Additionally, we identified five Y chromosome abnormalities in which G-banding could not distinguish their origins for four of the five cases.</p> <p>Conclusions</p> <p>Our study demonstrates the successful application and strong potential of array-MLPA in clinical diagnosis and prenatal testing for rapid and sensitive chromosomal aneuploidy screening. Furthermore, we have developed a simple and rapid procedure for screening copy numbers on chromosomes 13, 18, 21, X, and Y using array-MLPA.</p

Segawa syndrome caused by TH gene mutation and its mechanism

Dopa-responsive dystonia (DRD), also known as Segawa syndrome, is a rare neurotransmitter disease. The decrease in dopamine caused by tyrosine hydroxylase (TH) gene mutation may lead to dystonia, tremor and severe encephalopathy in children. Although the disease caused by recessive genetic mutation of the tyrosine hydroxylase (TH) gene is rare, we found that the clinical manifestations of seven children with tyrosine hydroxylase gene mutations are similar to dopa-responsive dystonia. To explore the clinical manifestations and possible pathogenesis of the disease, we analyzed the clinical data of seven patients. Next-generation sequencing showed that the TH gene mutation in three children was a reported homozygous mutation (c.698G&gt;A). At the same time, two new mutations of the TH gene were found in other children: c.316_317insCGT, and c.832G&gt;A (p.Ala278Thr). We collected venous blood from four patients with Segawa syndrome and their parents for real-time quantitative polymerase chain reaction analysis of TH gene expression. We predicted the structure and function of proteins on the missense mutation iterative thread assembly refinement (I-TASSER) server and studied the conservation of protein mutation sites. Combined with molecular biology experiments and related literature analysis, the qPCR results of two patients showed that the expression of the TH gene was lower than that in 10 normal controls, and the expression of the TH gene of one mother was lower than the average expression level. We speculated that mutation in the TH gene may clinically manifest by affecting the production of dopamine and catecholamine downstream, which enriches the gene pool of Segawa syndrome. At the same time, the application of levodopa is helpful to the study, diagnosis and treatment of Segawa syndrome

Gene expression during preimplantation development in the mouse embryo

Mouse preimplantation development is marked with pronounced changes in the patterns of reprogramming of gene expression during distinct transitions, namely the maternal-to-zygotic transition, compaction and blastocyst formation. This work examines RNA transcript profiles during the different stages of mouse preimplantation development. Using microarray analysis, combined with functional genomics tools such as Expression Analysis Systematic Explorer (EASE) and Ingenuity Pathway Analysis (IPA), we characterized global changes in gene expression and identified biological processes that accompany and likely underlie these transitions. This study confirmed previously described processes and events, but more important, revealed new insights. Response to DNA damage and DNA repair genes are over-represented in the oocyte and may reflect the oocyte\u27s response to selective pressures to insure genomic integrity; fertilization results in changes in the transcript profile in the 1-cell embryo that are far greater than previously recognized; and genome activation during the 2-cell stage may not be as global and promiscuous as previously proposed, but rather more selective, with genes involved in transcription and RNA processing being preferentially expressed. Further transcription profiling in 1-cell and 2-cell mouse embryos treated with transcription inhibitor α-amanitin confirmed this finding and identified genes that are activated during the course of zygotic gene activation; for example, Myc and Hdac1 could be critical players involved in genome activation and repression in the preimplantation mouse embryo. This work also reports the development of a linear mRNA amplification method from small amounts of mouse oocytes and preimplantation embryos and the subsequent generation of oocyte-specific and 8-cell-specific cDNA libraries using suppression subtractive hybridization; and these libraries were partially characterized. This work represents an extensive study on the global and temporal patterns of gene expression in the mouse oocyte and early embryo stages. The results validate this hypothesis-generating approach by identifying genes involved in critical biological processes that can now be the subject of more traditional hypothesis-driven study

AI-based Intrusion Detection for Intelligence Internet of Vehicles

With the development of intelligent technologies, Internet of Things (IoT) opens up a new era in the field of automotive networks, namely Internet of Vehicles (IoV). The main goal of IoV is to provide a secure and reliable network to vehicles so that users can enjoy various services. However, vulnerabilities and incomplete protection mechanisms have led to a proliferation of security threats against IoV networks. Intrusion detection technology is an effective protection solution for IoV security, especially when Artificial Intelligence (AI) technology has been introduced into intrusion detection study. This paper first briefly introduces the concept and features of IoV, and then reviews the related research on AI-based IoV intrusion detection systems (IDSs). Finally, we discuss the open challenges and future research directions