Amirhossein Afshinfard, S. Jackman, J. Wong, Lauren Coombe, Justin Chu, Vladimir Nikolić, Gokce Dilek, Yaman Malkoç, R. Warren, I. Birol
While conventional physical maps helped build most of the reference genomes we use today, generating the maps was prohibitively expensive, and the technology was abandoned in favor of whole-genome shotgun sequencing (WGS). However, genome assemblies generated using WGS data are often less contiguous. We introduce Physlr, a tool that leverages long-range information provided by some WGS technologies to construct next-generation physical maps. These maps have many potential applications in genome assembly and analysis, including, but not limited to, scaffolding. In this study, using experimental linked-read datasets from two humans, we used Physlr to construct chromosome-scale physical maps (NGA50s of 52 Mbp and 70 Mbp). We also demonstrated how these physical maps can help scaffold human genome assemblies generated using various sequencing technologies and assembly tools. Across all experiments, Physlr substantially improved the contiguity of baseline assemblies over state-of-the-art linked-read scaffolders.
{"title":"Physlr: Next-Generation Physical Maps","authors":"Amirhossein Afshinfard, S. Jackman, J. Wong, Lauren Coombe, Justin Chu, Vladimir Nikolić, Gokce Dilek, Yaman Malkoç, R. Warren, I. Birol","doi":"10.3390/dna2020009","DOIUrl":"https://doi.org/10.3390/dna2020009","url":null,"abstract":"While conventional physical maps helped build most of the reference genomes we use today, generating the maps was prohibitively expensive, and the technology was abandoned in favor of whole-genome shotgun sequencing (WGS). However, genome assemblies generated using WGS data are often less contiguous. We introduce Physlr, a tool that leverages long-range information provided by some WGS technologies to construct next-generation physical maps. These maps have many potential applications in genome assembly and analysis, including, but not limited to, scaffolding. In this study, using experimental linked-read datasets from two humans, we used Physlr to construct chromosome-scale physical maps (NGA50s of 52 Mbp and 70 Mbp). We also demonstrated how these physical maps can help scaffold human genome assemblies generated using various sequencing technologies and assembly tools. Across all experiments, Physlr substantially improved the contiguity of baseline assemblies over state-of-the-art linked-read scaffolders.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49165166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-05DOI: 10.48550/arXiv.2205.02610
Andreas Padalkin, C. Scheideler, Daniel Warner
The amoebot model [Derakhshandeh et al., 2014] has been proposed as a model for programmable matter consisting of tiny, robotic elements called amoebots. We consider the reconfigurable circuit extension [Feldmann et al., JCB 2022] of the geometric (variant of the) amoebot model that allows the amoebot structure to interconnect amoebots by so-called circuits. A circuit permits the instantaneous transmission of signals between the connected amoebots. In this paper, we examine the structural power of the reconfigurable circuits. We start with some fundamental problems like the stripe computation problem where, given any connected amoebot structure $S$, an amoebot $u$ in $S$, and some axis $X$, all amoebots belonging to axis $X$ through $u$ have to be identified. Second, we consider the global maximum problem, which identifies an amoebot at the highest possible position with respect to some direction in some given amoebot (sub)structure. A solution to this problem can then be used to solve the skeleton problem, where a (not necessarily simple) cycle of amoebots has to be found in the given amoebot structure which contains all boundary amoebots. A canonical solution to that problem can then be used to come up with a canonical path, which provides a unique characterization of the shape of the given amoebot structure. Constructing canonical paths for different directions will then allow the amoebots to set up a spanning tree and to check symmetry properties of the given amoebot structure. The problems are important for a number of applications like rapid shape transformation, energy dissemination, and structural monitoring. Interestingly, the reconfigurable circuit extension allows polylogarithmic-time solutions to all of these problems.
变形虫模型[Derakhshandeh et al.，2014]已被提出作为一种由称为变形虫的微小机器人元件组成的可编程物质的模型。我们考虑了几何（变体）变形虫模型的可重构电路扩展[Feldmann等人，JCB 2022]，该模型允许变形虫结构通过所谓的电路互连变形虫。电路允许在连接的变形虫之间即时传输信号。在本文中，我们考察了可重构电路的结构功率。我们从一些基本问题开始，比如条纹计算问题，其中，给定任何连接的变形虫结构$S$、$S$中的变形虫$u$和一些轴$X$，所有属于轴$X$~$u$的变形虫都必须被识别。其次，我们考虑全局最大值问题，该问题确定了在某个给定的变形虫（子）结构中，相对于某个方向处于最高可能位置的变形虫。然后可以使用该问题的解决方案来解决骨架问题，其中必须在包含所有边界变形虫的给定变形虫结构中找到变形虫的（不一定是简单的）循环。然后，可以使用该问题的规范解决方案来提出规范路径，该路径提供了给定变形虫结构形状的独特特征。构造不同方向的规范路径将允许变形虫建立生成树并检查给定变形虫结构的对称性。这些问题对于快速形状转换、能量传播和结构监测等许多应用都很重要。有趣的是，可重新配置的电路扩展允许所有这些问题的多对数时间解决方案。
{"title":"The Structural Power of Reconfigurable Circuits in the Amoebot Model","authors":"Andreas Padalkin, C. Scheideler, Daniel Warner","doi":"10.48550/arXiv.2205.02610","DOIUrl":"https://doi.org/10.48550/arXiv.2205.02610","url":null,"abstract":"The amoebot model [Derakhshandeh et al., 2014] has been proposed as a model for programmable matter consisting of tiny, robotic elements called amoebots. We consider the reconfigurable circuit extension [Feldmann et al., JCB 2022] of the geometric (variant of the) amoebot model that allows the amoebot structure to interconnect amoebots by so-called circuits. A circuit permits the instantaneous transmission of signals between the connected amoebots. In this paper, we examine the structural power of the reconfigurable circuits. We start with some fundamental problems like the stripe computation problem where, given any connected amoebot structure $S$, an amoebot $u$ in $S$, and some axis $X$, all amoebots belonging to axis $X$ through $u$ have to be identified. Second, we consider the global maximum problem, which identifies an amoebot at the highest possible position with respect to some direction in some given amoebot (sub)structure. A solution to this problem can then be used to solve the skeleton problem, where a (not necessarily simple) cycle of amoebots has to be found in the given amoebot structure which contains all boundary amoebots. A canonical solution to that problem can then be used to come up with a canonical path, which provides a unique characterization of the shape of the given amoebot structure. Constructing canonical paths for different directions will then allow the amoebots to set up a spanning tree and to check symmetry properties of the given amoebot structure. The problems are important for a number of applications like rapid shape transformation, energy dissemination, and structural monitoring. Interestingly, the reconfigurable circuit extension allows polylogarithmic-time solutions to all of these problems.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45008665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA nanoengineering, in particular, DNA origami has potential applications in a variety of areas including, for example, nanoelectronics, biomedical diagnostics, and therapeutics. To fully realize the potential of DNA self-assembly in these and other areas, methods must be available for economical, scalable, and reliable production of single-stranded DNA (ssDNA) scaffolds from virtually any source. In this review, we will describe the virtues and liabilities of four strategies for generating ssDNA, including Rolling Circle Amplification (RCA), strand-specific exonuclease digestion, chemical denaturation, and asymmetric PCR (aPCR), with suggestions for approaches to optimize the use of each method.
{"title":"A Comparison of Methods for the Production of Kilobase-Length Single-Stranded DNA","authors":"Chang-Yong Oh, E. Henderson","doi":"10.3390/dna2010005","DOIUrl":"https://doi.org/10.3390/dna2010005","url":null,"abstract":"DNA nanoengineering, in particular, DNA origami has potential applications in a variety of areas including, for example, nanoelectronics, biomedical diagnostics, and therapeutics. To fully realize the potential of DNA self-assembly in these and other areas, methods must be available for economical, scalable, and reliable production of single-stranded DNA (ssDNA) scaffolds from virtually any source. In this review, we will describe the virtues and liabilities of four strategies for generating ssDNA, including Rolling Circle Amplification (RCA), strand-specific exonuclease digestion, chemical denaturation, and asymmetric PCR (aPCR), with suggestions for approaches to optimize the use of each method.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46297874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Carrillo-Ávila, P. Catalina, R. Aguilar-Quesada
Cell lines are a widely used pre-clinical models for biomedical research. The accessibility and the relative simplicity of facilities necessary for the use of cell lines, along with the large number of potential applications, encourage many researchers to choose this model. However, the access to cell lines from a non-confident source or through the interlaboratory exchange results in uncontrollable cell lines of uncertain quality. Furthermore, the possibility of using cell lines as an endless resource through multiple passages can contribute to this uncontrolled scenario, the main consequence of which is the lack of reproducibility between the research results. Different initiatives have emerged to promote the best practices regarding the use of cell lines and minimize the effect on the scientific results reported, including comprehensive quality control in the frame of Good Cell Culture Practice (GCCP). Cell Banks, research infrastructures for the professional distribution of biological material of high and known quality and origin, are committed with these initiatives. Many of the quality controls used to test different attributes of cell lines are based on DNA. This review describes quality control protocols of cell lines whose target molecule is DNA, and details the scope or purpose and their corresponding functionality.
{"title":"Quality Control of Cell Lines Using DNA as Target","authors":"J. Carrillo-Ávila, P. Catalina, R. Aguilar-Quesada","doi":"10.3390/dna2010004","DOIUrl":"https://doi.org/10.3390/dna2010004","url":null,"abstract":"Cell lines are a widely used pre-clinical models for biomedical research. The accessibility and the relative simplicity of facilities necessary for the use of cell lines, along with the large number of potential applications, encourage many researchers to choose this model. However, the access to cell lines from a non-confident source or through the interlaboratory exchange results in uncontrollable cell lines of uncertain quality. Furthermore, the possibility of using cell lines as an endless resource through multiple passages can contribute to this uncontrolled scenario, the main consequence of which is the lack of reproducibility between the research results. Different initiatives have emerged to promote the best practices regarding the use of cell lines and minimize the effect on the scientific results reported, including comprehensive quality control in the frame of Good Cell Culture Practice (GCCP). Cell Banks, research infrastructures for the professional distribution of biological material of high and known quality and origin, are committed with these initiatives. Many of the quality controls used to test different attributes of cell lines are based on DNA. This review describes quality control protocols of cell lines whose target molecule is DNA, and details the scope or purpose and their corresponding functionality.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41601671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To date, our understanding of how DNA is packaged in the cell nucleus, condensed from chromatin into chromosomes, and organized throughout the cell cycle remains sparse. Three dimensional (3D) ultrastructural imaging is an important tool for unravelling the organizational structure of chromosomes. For large volume 3D imaging of biological samples, serial block-face scanning electron microscopy (SBFSEM) has been applied, whereby ultrastructural information is achieved by analyzing 3D reconstructions acquired from measured data sets. In this review, we summarize the contribution of SBFSEM for obtaining 3D images of chromosomes to investigate their ultrastructure and organization in the cell and its nucleus. Furthermore, this review highlights the potential of SBFSEM for advancing 3D chromosome research.
{"title":"3D Ultrastructural Imaging of Chromosomes Using Serial Block-Face Scanning Electron Microscopy (SBFSEM)","authors":"M. Yusuf, A. Sajid, I. Robinson, E. Lalani","doi":"10.3390/dna2010003","DOIUrl":"https://doi.org/10.3390/dna2010003","url":null,"abstract":"To date, our understanding of how DNA is packaged in the cell nucleus, condensed from chromatin into chromosomes, and organized throughout the cell cycle remains sparse. Three dimensional (3D) ultrastructural imaging is an important tool for unravelling the organizational structure of chromosomes. For large volume 3D imaging of biological samples, serial block-face scanning electron microscopy (SBFSEM) has been applied, whereby ultrastructural information is achieved by analyzing 3D reconstructions acquired from measured data sets. In this review, we summarize the contribution of SBFSEM for obtaining 3D images of chromosomes to investigate their ultrastructure and organization in the cell and its nucleus. Furthermore, this review highlights the potential of SBFSEM for advancing 3D chromosome research.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48916540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. A. Barcellos, M. S. de Souza, Victoria Tura, Larissa Rodrigues Pereira, Rafael Kretschmer, R. J. Gunski, A. D. Garnero
Avian cell culture is widely applied for cytogenetic studies, the improvement of which increasingly allows for the production of high-quality chromosomes, essential to perform both classical and molecular cytogenetic studies. Among these approaches, there are two main types: fibroblast and bone marrow culture. Despite its high cost and complexity, fibroblast culture is considered the superior approach due to the quality of the metaphases produced. Short-term bone marrow cultivation provides more condensed chromosomes but nonetheless is quicker and easier. In the search for a quicker, cheaper way to prepare metaphases without losing quality, the present work developed a novel, widely applicable protocol for avian chromosome preparation. Twenty-one bird embryos from distinct families were sampled: Icteridae, Columbidae, Furnariidae, Estrildidae, Thraupidae, Troglodytidae and Ardeidae. The protocol was based on a combination of modified fibroblast culture and bone marrow cultivation, taking the advantages of both. The results show that all species consistently presented good mitotic indexes and high-quality chromosomes. Overall, the application of this protocol for bird cytogenetics can optimize the time, considering that most fibroblast cultures take at least 3 days and often much longer. However, our protocol can be performed in 3 h with a much-reduced cost of reagents and equipment.
{"title":"Direct Chromosome Preparation Method in Avian Embryos for Cytogenetic Studies: Quick, Easy and Cheap","authors":"S. A. Barcellos, M. S. de Souza, Victoria Tura, Larissa Rodrigues Pereira, Rafael Kretschmer, R. J. Gunski, A. D. Garnero","doi":"10.3390/dna2010002","DOIUrl":"https://doi.org/10.3390/dna2010002","url":null,"abstract":"Avian cell culture is widely applied for cytogenetic studies, the improvement of which increasingly allows for the production of high-quality chromosomes, essential to perform both classical and molecular cytogenetic studies. Among these approaches, there are two main types: fibroblast and bone marrow culture. Despite its high cost and complexity, fibroblast culture is considered the superior approach due to the quality of the metaphases produced. Short-term bone marrow cultivation provides more condensed chromosomes but nonetheless is quicker and easier. In the search for a quicker, cheaper way to prepare metaphases without losing quality, the present work developed a novel, widely applicable protocol for avian chromosome preparation. Twenty-one bird embryos from distinct families were sampled: Icteridae, Columbidae, Furnariidae, Estrildidae, Thraupidae, Troglodytidae and Ardeidae. The protocol was based on a combination of modified fibroblast culture and bone marrow cultivation, taking the advantages of both. The results show that all species consistently presented good mitotic indexes and high-quality chromosomes. Overall, the application of this protocol for bird cytogenetics can optimize the time, considering that most fibroblast cultures take at least 3 days and often much longer. However, our protocol can be performed in 3 h with a much-reduced cost of reagents and equipment.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48789546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dimitrios S. Kanakoglou, Andromachi Pampalou, Lina S. Malakou, E. Lakiotaki, T. Loupis, Dimitrios M. Vrachnos, Panayiotis D. Glekas, Alexia Klonou, A. Giannopoulou, Madison Carpenter, P. Korkolopoulou, C. Piperi
Zinc fingers consist of one of the most abundant motifs in transcription factors and DNA-binding proteins. Recent studies provide evidence on the pathological implication of zinc finger proteins in various neurodevelopmental disorders and malignancies but their role in pediatric brain tumors is largely unexplored. To this end, we investigated the differential expression of zinc finger-containing genes along with relevant biological processes and pathways among four main brain tumor categories (pilocytic astrocytomas, ependymomas, medulloblastomas and glioblastomas). By employing an extended bioinformatic toolset, we performed a preliminary in silico study in order to identify the expression of zinc finger-containing genes and associated functions in pediatric brain tumors. Our data analysis reveals the prominent role of C2H2-type zinc finger-containing genes in the molecular mechanisms underlying pediatric brain tumors followed by the Ring and PHD finger types. Significant dysregulation of ABLIM2 and UHFR1 genes was detected in all tumor types drawing attention to the dysregulation of cell polarization process and Ubiquitin-Proteasome System (UPS) in the pathogenesis of pediatric brain tumors. Moreover, significant gene clustering was observed in multiple locations with two highly visible clusters revealing a contrast in gene regulation between medulloblastomas and the other three brain tumor types, indicating a promising area of future research.
{"title":"Central Role of C2H2-Type Zinc Finger-Containing Genes in Pediatric Brain Tumors","authors":"Dimitrios S. Kanakoglou, Andromachi Pampalou, Lina S. Malakou, E. Lakiotaki, T. Loupis, Dimitrios M. Vrachnos, Panayiotis D. Glekas, Alexia Klonou, A. Giannopoulou, Madison Carpenter, P. Korkolopoulou, C. Piperi","doi":"10.3390/dna2010001","DOIUrl":"https://doi.org/10.3390/dna2010001","url":null,"abstract":"Zinc fingers consist of one of the most abundant motifs in transcription factors and DNA-binding proteins. Recent studies provide evidence on the pathological implication of zinc finger proteins in various neurodevelopmental disorders and malignancies but their role in pediatric brain tumors is largely unexplored. To this end, we investigated the differential expression of zinc finger-containing genes along with relevant biological processes and pathways among four main brain tumor categories (pilocytic astrocytomas, ependymomas, medulloblastomas and glioblastomas). By employing an extended bioinformatic toolset, we performed a preliminary in silico study in order to identify the expression of zinc finger-containing genes and associated functions in pediatric brain tumors. Our data analysis reveals the prominent role of C2H2-type zinc finger-containing genes in the molecular mechanisms underlying pediatric brain tumors followed by the Ring and PHD finger types. Significant dysregulation of ABLIM2 and UHFR1 genes was detected in all tumor types drawing attention to the dysregulation of cell polarization process and Ubiquitin-Proteasome System (UPS) in the pathogenesis of pediatric brain tumors. Moreover, significant gene clustering was observed in multiple locations with two highly visible clusters revealing a contrast in gene regulation between medulloblastomas and the other three brain tumor types, indicating a promising area of future research.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43248123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"One for Sorrow","authors":"D. Griffin","doi":"10.3390/dna1020011","DOIUrl":"https://doi.org/10.3390/dna1020011","url":null,"abstract":"“Did it work [...]","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42934650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Research Question: Is maternal age only a gross predictor of chromosome abnormalities in human embryos? Design: Here, we evaluated the less-studied variation in chromosome abnormality rates in embryos of patients within the same age group. Patients undergoing IVF and PGD for chromosomal abnormalities in ~127 different IVF clinics were included. PGT-A analysis was performed by a single reference laboratory using array CGH or NGS. To get an estimate of the range of abnormalities observed, the aCGH and NGS data were studied both independently and together. Results: The overall results showed the typical increase in aneuploidy rates with advancing maternal age (AMA) but extensive variability within each age group. Conclusions: Increasing aneuploidy with maternal age has been demonstrated in live births, unborn fetuses, IVF embryos and oocytes. In contrast, post-meiotic and other abnormalities that might lead to mosaicism, polyploidy and haploidy, are commonplace (around 30%), regardless of maternal age. Here we conclude that age is only a gross predictor of chromosome abnormalities in IVF embryos. In contrast to the existing standard of offering PGT-A to AMA patients, the high rate and extreme variation of chromosomal abnormalities in human embryos may warrant PGT-A for further IVF cycles even in younger age groups, especially if a history of increased levels of aneuploidy is evident. Furthermore, better indicators are needed to determine which patients are at a higher risk of producing increased levels of aneuploid embryos.
{"title":"Large Intra-Age Group Variation in Chromosome Abnormalities in Human Blastocysts","authors":"S. Sawarkar, D. Griffin, L. Ribustello, S. Munné","doi":"10.3390/dna1020010","DOIUrl":"https://doi.org/10.3390/dna1020010","url":null,"abstract":"Research Question: Is maternal age only a gross predictor of chromosome abnormalities in human embryos? Design: Here, we evaluated the less-studied variation in chromosome abnormality rates in embryos of patients within the same age group. Patients undergoing IVF and PGD for chromosomal abnormalities in ~127 different IVF clinics were included. PGT-A analysis was performed by a single reference laboratory using array CGH or NGS. To get an estimate of the range of abnormalities observed, the aCGH and NGS data were studied both independently and together. Results: The overall results showed the typical increase in aneuploidy rates with advancing maternal age (AMA) but extensive variability within each age group. Conclusions: Increasing aneuploidy with maternal age has been demonstrated in live births, unborn fetuses, IVF embryos and oocytes. In contrast, post-meiotic and other abnormalities that might lead to mosaicism, polyploidy and haploidy, are commonplace (around 30%), regardless of maternal age. Here we conclude that age is only a gross predictor of chromosome abnormalities in IVF embryos. In contrast to the existing standard of offering PGT-A to AMA patients, the high rate and extreme variation of chromosomal abnormalities in human embryos may warrant PGT-A for further IVF cycles even in younger age groups, especially if a history of increased levels of aneuploidy is evident. Furthermore, better indicators are needed to determine which patients are at a higher risk of producing increased levels of aneuploid embryos.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43895256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-11-17DOI: 10.4230/LIPIcs.DNA.2020.10
D. Caballero, Timothy Gomez, R. Schweller, Tim Wylie
Many models of self-assembly have been shown to be capable of performing computation. Tile Automata was recently introduced combining features of both Celluar Automata and the 2-Handed Model of self-assembly both capable of universal computation. In this work we study the complexity of Tile Automata utilizing features inherited from the two models mentioned above. We first present a construction for simulating Turing Machines that performs both covert and fuel efficient computation. We then explore the capabilities of limited Tile Automata systems such as 1-Dimensional systems (all assemblies are of height 1) and freezing Systems (tiles may not repeat states). Using these results we provide a connection between the problem of finding the largest uniquely producible assembly using n states and the busy beaver problem for non-freezing systems and provide a freezing system capable of uniquely assembling an assembly whose length is exponential in the number of states of the system. We finish by exploring the complexity of the Unique Assembly Verification problem in Tile Automata with different limitations such as freezing and systems without the power of detachment. 2012 ACM Subject Classification Theory of computation → Turing machines; Computer systems organization → Molecular computing; Theory of computation → Problems, reductions and completeness
{"title":"Verification and Computation in Restricted Tile Automata","authors":"D. Caballero, Timothy Gomez, R. Schweller, Tim Wylie","doi":"10.4230/LIPIcs.DNA.2020.10","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.2020.10","url":null,"abstract":"Many models of self-assembly have been shown to be capable of performing computation. Tile Automata was recently introduced combining features of both Celluar Automata and the 2-Handed Model of self-assembly both capable of universal computation. In this work we study the complexity of Tile Automata utilizing features inherited from the two models mentioned above. We first present a construction for simulating Turing Machines that performs both covert and fuel efficient computation. We then explore the capabilities of limited Tile Automata systems such as 1-Dimensional systems (all assemblies are of height 1) and freezing Systems (tiles may not repeat states). Using these results we provide a connection between the problem of finding the largest uniquely producible assembly using n states and the busy beaver problem for non-freezing systems and provide a freezing system capable of uniquely assembling an assembly whose length is exponential in the number of states of the system. We finish by exploring the complexity of the Unique Assembly Verification problem in Tile Automata with different limitations such as freezing and systems without the power of detachment. 2012 ACM Subject Classification Theory of computation → Turing machines; Computer systems organization → Molecular computing; Theory of computation → Problems, reductions and completeness","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46766687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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