척추동물아문 내 다른 계통 간 대진화를 이해하기 위한 생물정보학적 접근

학위논문(박사) -- 서울대학교대학원 : 자연과학대학 협동과정 생물정보학전공, 2022. 8. 김희발.생물정보학은 디지털화된 유전서열정보를 토대로 다양한 생명현상의 원리를 규명하고 이를 활용해 인류의 삶의 질을 향상하는 것을 목적으로 할 것이다. 생물정보학적 연구는 각 종을 대표하는 표준유전체 구축으로 일반적으로 시작되고 미소 혹은 대진화에 대한 후속 연구를 진행한다. 비록 짧은 단편 해독 기술이 유전체 시대를 열었지만, 짧은 단편의 조립은 낮은 연결성이나 오류가 포함된 유전자 주석 등의 심각한 문제들을 가진다. 긴 단편 해독 기술은 염색체 수준의 주석 (scaffolds)에 필수적인 보다 긴 컨티그 (contig) 조립을 생산할 수 있다. 짧은 단편에서 긴 단편으로 변화하는 페러다임에 발 맞추어, 본 논문은 표준유전체 구축에서 비교유전체 분석까지 이어지는 일련의 생물정보학적 분석에 대한 집약적 연구를 수행했으며, 이는 다양한 척추동물 종들의 대진화를 이해하는 것이 목적이다. 제 1장에서는 연구의 일반적인 배경지식을 정리하였다. 첫째로, 염색체 수준의 주석을 달성한 표준유전체 구축의 페러다임 변화를 설명했다. 다음으로, 특이적 형질에 관련된 분자 진화를 규명하는 비교유전체 분석 방법 및 사례를 정리했다. 제 2장에서는 표준유전체를 구축한 사례로서, 대한민국의 고유종인 큰볏말뚝망둥어의 염색체 수준 표준유전체를 구축했다. 척추동물 유전체 프로젝트와 국제 협력을 통해 4가지 최신 유전체 해독기술들 (Pacbio CLR, 10X Genomics linked reads, Bionano optical mapping, 그리고 Arima Genomics Hi-C)을 활용하여, 기존 표준유전체와 비교해 연결성 (continuity, Scaffold N50 기준)이 약 100배 향상되고 총 25개의 염색체를 가진 고품질 표준유전체를 완성했다. 또한, Pacbio Isoseq전사체 데이터를 유전자 주석에 활용하여 총 24,744개의 유전자를 발굴했다. 제 3장에서는 표준유전체 품질 평가 방법과 비교유전체학적 분석을 접목한 사례로서, 분화 시기가 오래된 종 간에도 BUSCO 유전자를 활용해 염색체 수준의 진화 양상을 탐색하는 방법과 척추동물 내에서 사례를 제시했다. 또한, 포유류, 조류, 어류 등 다양한 척추동물의 표준유전체에서 후속 분석 상의 문제를 야기하는 허위 소실 및 중복 오류를 탐색하는 방법과 사례를 제시하고 발생원인을 밝혔다. 제 4장에서는 기존의 비교유전체학적 분석을 적용한 사례로서, 실러캔스를 포함하는 육기아강 단계통 파생적 진화에 대한 분석을 통해 육상 적응 및 사지 출현의 분자 기작을 규명했다. 제 5장에서는 새로운 비교유전체학적 분석을 적용한 사례로서, 발성학습 조류 및 대조군 각각의 다계통 수렴 진화에 대한 분석을 통해 아미노산 수렴의 진화적 법칙을 제안하고 발성 학습에 연관된 후보 유전자를 발굴했다. 이러한 표준유전체 구축에서부터 비교유전체 분석으로 이어지는 생물정보학적 접근을 통해 규명된 주요 연구결과 중에, 염색체 상 텔로미어 서열 분포 및 아미노산 수렴 진화의 원리는 척추동물 외에 다른 분류 군에서도 비교될 기준이 될 수 있을 것으로 기대된다. 또한, 사지 발달 및 발성 학습에 연관된 후보 유전자를 발굴한 비교유전체학적 접근법은 전 세계 다양한 생물들의 다양한 유용 형질에 연관된 유용 유전자를 발굴하는데 활용될 수 있을 것이다.Bioinformatics aims to improve the quality of life of mankind by decoding molecular mechanisms of biological phenomena based on digitalized sequence information of various species. It generally begins with a construction of reference genomes representing each species and moves on downstream analyses for microevolution within species and macroevolutions between species. Although short-read sequencing technologies initiated genomics era, the short read assemblies had critical problems for lower continuity and erroneous gene annotations causing mis-interpretations. Long read sequencing technologies improved assembly continuities fundamental to chromosome-level scaffolds and corrected false annotations. Following up the paradigm shift from short-reads to long-reads, here, I performed a series of bioinformatic analyses to understand macroevolutions of various vertebrate species from reference genome construction to comparative genome approaches. Chapter 1 summarized the general background of this dissertation. First, it described the paradigm shift of the reference genome constructions achieving chromosome-scale scaffolds. Next, comparative genomic approaches for specific traits were summarized. Chapter 2, as a case of constructing a reference genome, illuminated a chromosome-level reference genome of giant-fin mudskipper, an endemic species in republic of Korea. Based on the four latest genome sequencing technologies (Pacbio CLR, 10X Genomics linked reads, Bionano optical mapping, and Arima Genomics Hi-C) in the international cooperation with the Vertebrate genomes project, it improved the 100-fold longer continuity (Scaffold N50) with a total of 25 chromosomal-level scaffolds compared to that of the previous genome. In addition, a total of 24,744 genes were annotated with Pacbio Isoseq transcriptome data. In Chapter 3, as a case of combining the reference genome quality evaluation method and comparative genomic analyses, a method was developed to explore the chromosomal evolution between vertebrate species in distant lineages focusing on the BUSCO genes. In addition, it suggested methods for detecting false loss and duplication errors that cause problems in downstream analyses in reference genomes of various vertebrate lineages, such as, mammals, birds, and fishes, and revealed how those kinds of errors occurred. In Chapter 4, as a case using the existing comparative genomic approaches, the molecular mechanisms of terrestrial adaptation and limb emergence were identified by applying the series of analyses for apormorphic evolution of the monophyletic lineage of lobed-fin fishes including coelacanths and human. In Chapter 5, as a case developing a new comparative genomic approach, the rule of amino acid convergence was proposed and candidate genes related to vocal learning were discovered through the multi-omic analyses for convergent evolution between polyphyletic lineages of vocal learning bird and control groups. Among the major findings of this study based on the bioinformatics approaches from the reference genome construction to comparative genomic researches, telomere sequence distributions on chromosomes and the principles of amino acid convergence would be a standard for comparisons in various lineages. In addition, the systemized comparative genomic approaches that identified candidate genes involved in limb development and vocal learning may be utilized to discover new candidate genes associated with various useful traits of living things in the world.Chapter 1. LITERATURE REVIEW 1 1.1 Paradigm shift in reference genome constructions 2 1.2 Comparative genomics for specific traits 3 Chapter 2. CHROMOSOME-LEVEL GENOME ASSEMBLY OF PERIOPHTHALMUS MAGNUSPINNATUS: AN INDIGENOUS MUDSKIPPER IN THE YELLOW SEA 5 2.1 Abstract 6 2.2 Introduction 7 2.3 Materials and Methods 9 2.4 Results and Discussion 13 Chapter 3. COMPARATIVE GENOMIC APPROACHES TO DETECT ERRONEOUS GENES IN REFERENCE GENOMES AND TO VISUALIZE CHROMOSOME EVOLUTION ACROSS VERTEBRATES 24 3.1 Abstract 25 3.2 Introduction 26 3.3 Materials and Methods 28 3.4 Results and Discussion 32 Chapter 4. COELACANTH-SPECIFIC ADAPTIVE GENES GIVE INSIGHTS INTO PRIMITIVE EVOLUTION FOR WATER-TO-LAND TRANSITION OF TETRAPODS 59 4.1 Abstract 60 4.2 Introduction 61 4.3 Materials and Methods 63 4.4 Results 69 4.5 Discussion 79 Chapter 5. AMINO ACID CONVERGENCES BETWEEN INDEPENDENT LINEAGES IN BIRDS GIVE EVOLUTIONARY INSIGHTS INTO AVIAN VOCAL LEARNING 85 5.1 Abstract 86 5.2 Introduction 87 5.3 Materials and Methods 89 5.4 Results 98 5.5 Discussion 159 GENERAL DISCUSSUSION 167 REFERENCES 168 요약(국문초록) 176박

Proceedings of the First NASA Formal Methods Symposium

Topics covered include: Model Checking - My 27-Year Quest to Overcome the State Explosion Problem; Applying Formal Methods to NASA Projects: Transition from Research to Practice; TLA+: Whence, Wherefore, and Whither; Formal Methods Applications in Air Transportation; Theorem Proving in Intel Hardware Design; Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering; Model Checking for Autonomic Systems Specified with ASSL; A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process; Software Model Checking Without Source Code; Generalized Abstract Symbolic Summaries; A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing; Component-Oriented Behavior Extraction for Autonomic System Design; Automated Verification of Design Patterns with LePUS3; A Module Language for Typing by Contracts; From Goal-Oriented Requirements to Event-B Specifications; Introduction of Virtualization Technology to Multi-Process Model Checking; Comparing Techniques for Certified Static Analysis; Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder; jFuzz: A Concolic Whitebox Fuzzer for Java; Machine-Checkable Timed CSP; Stochastic Formal Correctness of Numerical Algorithms; Deductive Verification of Cryptographic Software; Coloured Petri Net Refinement Specification and Correctness Proof with Coq; Modeling Guidelines for Code Generation in the Railway Signaling Context; Tactical Synthesis Of Efficient Global Search Algorithms; Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems; and Formal Methods for Automated Diagnosis of Autosub 6000

A Study on Adaptive Strategies of Wild and Cultivated Linum Populations Across Western Europe and Their Implications for Linum Trait Development and Ecology.

Local adaptation plays a major part in plant survival and reproduction. Linum represents a genus of potential study models which provide insights for both applied and evolutionary biology. As a flowering plant, they may have evolved adaptations to achieve optimal flowering time. Most flowering plants have developed their own strategies to flower in specific habitats. There are interests from both evolutionary, and agricultural points of view regarding flowering development. In evolutionary terms, flowering time may affect offspring and population fitness. In agriculture, faster flowering time is a desirable trait for production. For this reason, Linum is a versatile model to study. Linum usitatissimum (cultivated flax) is useful in several industries. Their wild predecessors, the wild flax (Linum bienne) is relatively less studied in comparison to their cultivated relative. As their predecessor, we suggest that implications of local adaptation in the wild flax, may aid the development of their cultivar relatives. We examined both wild and cultivar type to determine local adaptation strategies, particularly in terms of flowering. In chapter 2 of this thesis, we examined three flowering time genes and two duplicate genes. Linum is a temperate plant and as such requires vernalization. Vernalization is the process in which plants require colder temperatures to induce the flowering process. Plants that require vernalization often flower earlier when in colder temperatures than those that have not experienced cold induction. We studied expression of five flowering time genes for implication of local adaptation after treatment to vernalization. L. bienne appeared to express genes differently in comparison to the cultivars. The expression of Linum FLOWERING LOCUS T (LuFT) revealed a positive correlation with number of days to flower. This potentially identifies FLOWERING LOCUS T as one of the important genes regulating vernalization in Linum. Our result revealed variation in relative flowering time gene expressions. Wild and cultivated Linum demonstrate different relationships between flowering time and environmental variables. In chapter 3, we quantified the viability of pollen, an important part in the transfer of the male gamete in flowering plants, under different temperature treatments. Linum is an established temperate plant. Sensitivity to temperature changes maybe more predominant in temperate plants as seasonal changes would reflect a challenge to flower in temperate environments. In this chapter, Linum pollen was treated under different temperatures to observe their ability to germinate. This is important to determine whether temperature plays a major part in affecting the viability of pollen, which in turn plays a major role in the formation of seeds. This chapter revealed a reduction in the number of pollen tubes formed under different treatments and across the two Linum species. In addition to this, correlations to local climates were also observed, with variation in trends across the temperature treatments. In chapter 4 of this thesis, we examined population genetics of wild L. bienne samples originating from different latitudes across western Europe. We examined Wild flax (L. bienne) populations across western Europe to provide insights into their genetic structure and diversity. This population analysis will develop our understanding of adaptation in wild Linum in response to their environment. A double-digest RAD sequencing (DDRadSeq) protocol was utilized to look at variation in SNPs across different populations. Both L. bienne and L. usitatissimum samples were sequenced and aligned to an L. usitatissimum whole genome. Genetic structuring of our Linum samples were revealed across Western Europe. Cultivars in our collection revealed to be more genetically related to the Northern accessions of our wild samples. In chapter 5 we summarized plant architectures. In this chapter traits and their relationship to the latitude were summarized in relation to the requirement for vernalization. Four traits were measured: overall height of the plants after first flowering, the number of stems of the plants after first flowering, and the number of flower buds on the plants at first flowering. In addition to this, seed size was examined in terms of its area. We also examined correlation between traits and environmental variables. We found that there was a relationship between traits when no-vernalization occurred. With vernalization, these relationships became less significant and, in some cases, not significant. This illustrates that vernalization influences the relationship of traits beyond flowering initiation. There were also suggestions that the traits measured correlate with latitude under no-vernalization treatments. For vernalized individuals, the correlation for the traits measured and latitude was not significant. Seed sizes were strongly correlated with both latitude and climatic variables in all cases of the treatments. The findings suggest there are effect of environmental variables in these measured traits, which suggests differentiation within wild Linum species

Tools and Algorithms for the Construction and Analysis of Systems

This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

Tools and Algorithms for the Construction and Analysis of Systems

This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

Acute Leukemia

This book provides a comprehensive overview of he basic mechanisms underlying areas of acute leukemia, current advances, and future directions in management of this disease. The first section discusses the classification of acute leukemia, taking into account diagnoses dependent on techniques that are essential, and thankfully readily available, in the laboratory. The second section concerns recent advances in molecular biology, markers, receptors, and signaling molecules responsible for disease progression, diagnostics based on biochips and other molecular genetic analysis. These advances provide clinicians with important understanding and improved decision making towards the most suitable therapy for acute leukemia. Biochemical, structural, and genetic studies may bring a new era of epigenetic based drugs along with additional molecular targets that will form the basis for novel treatment strategies. Later in the book, pediatric acute leukemia is covered, emphasizing that children are not small adults when it comes to drug development. The last section is a collection of chapters about treatment, as chemotherapy-induced toxicity is still a significant clinical concern. The present challenge lies in reducing the frequency and seriousness of adverse effects while maintaining efficacy and avoiding over-treatment of patients