Celebrating the discovery of DNA demethylase

Maintaining correct DNA methylation patterns entails the addition of methyl groups by DNA methyltransferases and the active removal of methylation from DNA. Removing a methyl group from 5-methylcytosine requires breaking a strong C–C bond, suggesting that demethylation might occur by an alternative mechanism that does not involve severing this bond. Indeed, the discovery of the 5-methylcytosine DNA glycosylase (also known as DNA demethylase) REPRESSOR OF SILENCING 1 (ROS1) by (Gong et al., 2002) revolutionized thinking in this field, as the study of ROS1 revealed a mechanism by which 5-methylcytosine is excised and replaced by the DNA repair machinery. This special issue celebrates the 20th anniversary of the discovery of ROS1 and the remarkable research that followed.     

Conceptual biology,hypothesis discovery,and text mining: Swanson's legacy

Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians.     

The life and legacy of Marie Curie

Marie Curie was a remarkable woman whose discoveries broke new ground in physics and chemistry and also opened the door for advances in engineering, biology, and medicine. She broke new ground for women in science: she was, for example, the first woman to receive a doctor of science degree in France, the first woman to win Nobel Prize, the first woman to lecture at the Sorbonne, the first person to win two Nobel Prizes, and the first Nobel Laureate whose child also won a Nobel Prize. Her life offers insights into the changing role of women in science and academia over the past century. It also offers examples of many ways in which scientists can, and should, work to improve the educational programs and career opportunities available to those who follow in their footsteps.     

Trevor Alleyne Thorpe: His academic life and scientific legacy

In Vitro Cellular & Developmental Biology - Plant - This special review is written to commemorate the life and contributions of Dr. Trevor Alleyne Thorpe, who passed away on May 18, 2020, at...     

Platyhelminth systematics and the emergence of new characters

Since the inclusion of molecular data in modern phylogenetic analyses, significant progress in resolving the origins and radiation of flatworms has been made, although some key problems remain. Here I review developments in the supply and use of systematic characters that provide the basis for diagnosis and phylogeny reconstruction, that in turn have driven systematic revisions and the interpretation of broader evolutionary patterns and processes; focus is placed on the parasitic taxa. Although useful tools have been refined to the point of becoming established systematic markers of broad utility, attention to the need for denser gene and taxon sampling is addressed in the light of unresolved questions and current trends in molecular systematics, from nucleotide to genome. Tradition and the nature of available comparative information tends to dictate the choice of systematic markers, but faced with incongruent phylogenies, the emergence of new technologies and the need for rapid species diagnosis, there is a pressing need to assess and standardize our choice of tools so they are fit for purpose, available to all and used widely. I present a brief review of existing and potential sources of phylogenetic characters and discuss their likely value in the context of the systematics and diagnostics of parasitic flatworms.     

Personal reflections on the life and legacy of Alexander Hollaender

Mary Esther Gaulden presents a personal summary of the activities of Alexander Hollaender, from his days at the National Institutes of Health to his becoming Director of the Biology Division of the Oak Ridge National Laboratory in 1947. This appealing story deals with many of her reactions to his personality and organizational style. It reflects the atmosphere of science in those days, and her enthusiasm in this vibrant milieu. Next is a brief account by John Jagger of his first meeting with Dr. Hollaender, arrival in Oak Ridge in April 1956, and wedding to Mary Esther six months later at the house of the Hollaenders in Oak Ridge. The third section is an account by Virginia P. White of how she came to Oak Ridge in 1955 and became Dr. Hollaender's Laboratory Administrator. She gives a personal account of the many facets of his managerial style, as well as of the personality of his wife, Henrietta. She also describes one of Hollaender's many avocations, the collection of fossils on Sunday morning hikes in the Cumberland Mountains, accompanied by lab and visiting personnel, and finally comments on the annual research conferences in Gatlinburg TN, for which Hollaender and the lab became very well known, with some closing vignettes on his leadership style.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

Insect morphology in the age of phylogenomics: innovative techniques and its future role in systematics

A brief account of the history of insect morphology is given. Different techniques and analytical methods used in current projects on insect morphology and phylogeny and their optimized combined application are described. These include fixation, dissection, maceration, histology (microtome sectioning), scanning electron microscopy (SEM), transmission electron microscopy (TEM), serial block‐face scanning electron microscopy (SBFSEM), focused ion beam scanning electron microscopy (FIB/SEM), confocal laser scanning microscopy (CLSM), bleaching, micro‐computed tomography (μCT), computer‐based three‐dimensional reconstruction, focus stacking of digital images, geometric morphometrics and the storage of morphological metadata. The role of insect morphology in the “age of phylogenomics” is discussed.     

新世纪的中国昆虫系统学

对未来我国昆虫系统学在能力建设、物种编目、理论研究、技术创新和国际合作等方面提出一系列建议。在昆虫系统学能力建设方面,政府和科学家应该在生物分类学能力评估、基础硬件建设、各级生物标本馆中建立伙伴关系（包括标本采集、标本馆管理、 科学研究、 知识共享和标本与资料交换）等方面重点开展工作。在物种编目方面,我国的昆虫物种编目有赖于各级政府和机构继续关注标本的收集和保藏,继续启动一些考察项目,以满足发现和认识昆虫物种的实际需求。在物种水平上研究以往昆虫系统学家的工作,进行地区性和世界性的昆虫类群的订正更是非常必要的。在理论研究方面,我国昆虫系统应该在下列方面积极探索：物种概念、进化理论、比较生物学理论和高级分类系统研究。在技术创新方面,我国的昆虫系统学家应该在数据库与网络技术应用、图形图像处理技术、专家鉴定系统技术、分类性状分析技术、分子生物学技术、系统发育推断程序、信息统一管理技术和知识传播技术等方面进行深入研究,以满足昆虫系统学的发展需求。在国际合作方面,要进一步推动我国昆虫系统学研究机构加入生物分类学全球战略联盟、加入各种相关国际相关组织,要促进物种信息管理系统的建立与共享,要推动研究项目国际化。     

Celebrating the golden anniversary of the discovery of bacillosamine, the diamino sugar of a Bacillus

Bacillosamine (2,4-diamino-2,4,6-trideoxy-d-glucose, Bac), a rare amino sugar, was discovered 50 years ago as a result of the follow-up of a chance observation made during studies of polypeptide synthesis by a Bacillus subtilis strain later renamed Bacillus licheniformis. In the following decades this amino sugar was almost completely ignored, although it was found in a number of bacterial polysaccharides and other metabolites. Recently, there has been a burst of interest in Bac when it was found to be a link glycan in eubacterial glycoproteins. In this retrospective, I review the chance discovery of Bac, its structural determination and its biosynthesis.