组蛋白赖氨酸甲基化修饰与肿瘤

对组蛋白甲基化修饰认识已有相当长的时间,但直到最近几年由于组蛋白甲基化修饰酶的发现才使人们逐渐认识到组蛋白甲基化修饰有广泛的生物学功能,像异染色质形成、X染色体失活、转录调节、干细胞的维持和分化等,组蛋白甲基化修饰的改变与某些人类疾病和肿瘤也有一定关系。组蛋白修饰是可逆性的,这为某些疾病的治疗提供了新的可能。     

Molecular biology and Pauling's immunochemistry: a neglected dimension

This paper argues that there is a substantial overlap between the history of immunology and the history of molecular biology, an overlap manifested in the researches on antibodies during the 1930s and 1940s. This common ground is a product of intellectual developments, as well as institutional trends. Viewed from an intellectual vantage point of the 1930s and 1940s, molecular biology was essentially the study of the biological specificities of the so-called 'giant protein molecules'. Within the conceptual framework of early molecular biology, which was rooted in the protein view of life, the concepts of protein template, autocatalysis, and heterocatalysis were central in explaining the protein syntheses of genes, viruses, enzymes, hormones, and antibodies. Immunochemistry and serological genetics were at the heart of that research agenda. This paper also shows that the immunochemistry program of Linus Pauling, which focused on molecular mechanisms of antibody structure and function, and the projects in serological genetics at Caltech's biology division were supported by the Rockefeller Foundation under the aegis of its molecular biology program. Based on the close examination of intellectual and institutional factors, the histories of molecular biology and immunology in the pre-DNA era are seen as closely linked.     

Epigenetics and the maintenance of developmental plasticity: extending the signalling theory framework

Developmental plasticity, a phenomenon of importance in both evolutionary biology and human studies of the developmental origins of health and disease (DOHaD), enables organisms to respond to their environment based on previous experience without changes to the underlying nucleotide sequence. Although such phenotypic responses should theoretically improve an organism's fitness and performance in its future environment, this is not always the case. Herein, we first discuss epigenetics as an adaptive mechanism of developmental plasticity and use signaling theory to provide an evolutionary context for DOHaD phenomena within a generation. Next, we utilize signalling theory to identify determinants of adaptive developmental plasticity, detect sources of random variability – also known as process errors that affect maintenance of an epigenetic signal (DNA methylation) over time, and discuss implications of these errors for an organism's health and fitness. Finally, we apply life‐course epidemiology conceptual models to inform study design and analytical strategies that are capable of parsing out the potential effects of process errors in the relationships among an organism's early environment, DNA methylation, and phenotype in a future environment. Ultimately, we hope to foster cross‐talk and interdisciplinary collaboration between evolutionary biology and DOHaD epidemiology, which have historically remained separate despite a shared interest in developmental plasticity.     

Concordance in hippocampal and fecal Nr3c1 methylation is moderated by maternal behavior in the mouse

Recent advances in genomic technologies now enable a reunion of molecular and evolutionary biology. Researchers investigating naturally living animal populations are thus increasingly able to capitalize upon genomic technologies to connect molecular findings with multiple levels of biological organization. Using this vertical approach in the laboratory, epigenetic gene regulation has emerged as an important mechanism integrating genotype and phenotype. To connect phenotype to population fitness, however, this same vertical approach must now be applied to naturally living populations. A major obstacle to studying epigenetics in noninvasive samples is tissue specificity of epigenetic marks. Here, using the mouse as a proof‐of‐principle model, we present the first known attempt to validate an epigenetic assay for use in noninvasive samples. Specifically, we compare DNA methylation of the NGFI‐A (nerve growth factor‐inducible protein A) binding site in the promoter of the glucocorticoid receptor (Nr3c1) gene between central (hippocampal) and peripheral noninvasive (fecal) tissues in juvenile Balb/c mice that had received varying levels of postnatal maternal care. Our results indicate that while hippocampal DNA methylation profiles correspond to maternal behavior, fecal DNA methylation levels do not. Moreover, concordance in methylation levels between these tissues within individuals only emerges after accounting for the effects of postnatal maternal care. Thus, although these findings may be specific to the Nr3c1 gene, we urge caution when interpreting DNA methylation patterns from noninvasive tissues, and offer suggestions for further research in this field.     

Biological surfaces as catalysts of amyloid aggregate nucleation and primary sites of amyloid toxicity

The themes of protein folding, misfolding, aggregation and aggregate toxicity to living systems are among the most exciting frontiers in molecular and cell biology as well as in molecular medicine. This is testified by the increasingly higher number of publications on these issues and the debate in the scientific community about some basic questions still unresolved. One of the latter is the role performed in vitro by synthetic and in vivo by biological surfaces in favouring or disfavouring protein folding and misfolding, in speeding the rate of aggregate nucleation and as key targets of toxic aggregates. Indeed, recent research has highlighted the roles of surfaces in all these phenomena; it has also stressed that early oligomeric assemblies in the path of fibrillization are endowed with the highest cytotoxicity and that the latter most likely follows aggregate interaction with cell membrane(s). The resulting membrane destabilization and permeabilization with early alterations in intracellular redox status and ion homeostasis possibly culminates with cell death. Each of these steps is most likely influenced by the physicochemical and biochemical features of the membrane(s) themselves in ways that are still under investigation. This review summarizes the most recent advances in these fields.     

Chromatographic and electrophoretic characterization of protein variants

Almost all proteins are expressed in several variants, also known as isoforms. Individual protein variants differ by modifications of the individual amino acid side chains, or the N- or C-terminus. Typical modifications are glycosylation, phosphorylation, acetylation, methylation, deamidation or oxidation. It is of utmost interest to either get a quantitative picture of the variants of a particular protein or to separate the variants in order to be able to identify their molecular structure. Protein variants are present in native as well as in recombinant proteins. In the case of protein production it is interesting, how variants are generated during fermentation, purification processes, storage, and how present individual variants influence the biological activity. This review provides a comparison of chromatographic and electrophoretic separation methods to analyze and to prepare protein variants.     

Of truth and pathways: chasing bits of information through myriads of articles

Knowledge on interactions between molecules in living cells is indispensable for theoretical analysis and practical applications in modern genomics and molecular biology. Building such networks relies on the assumption that the correct molecular interactions are known or can be identified by reading a few research articles. However, this assumption does not necessarily hold, as truth is rather an emerging property based on many potentially conflicting facts. This paper explores the processes of knowledge generation and publishing in the molecular biology literature using modelling and analysis of real molecular interaction data. The data analysed in this article were automatically extracted from 50000 research articles in molecular biology using a computer system called GeneWays containing a natural language processing module. The paper indicates that truthfulness of statements is associated in the minds of scientists with the relative importance (connectedness) of substances under study, revealing a potential selection bias in the reporting of research results. Aiming at understanding the statistical properties of the life cycle of biological facts reported in research articles, we formulate a stochastic model describing generation and propagation of knowledge about molecular interactions through scientific publications. We hope that in the future such a model can be useful for automatically producing consensus views of molecular interaction data.     

From molecules to dynamic biological communities

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.     

Fluorescent oligo and poly-thiophenes and their utilization for recording biological events of diverse origin—when organic chemistry meets biology

The technique of using luminescent oligo-thiophenes and luminescent conjugated poly-thiophenes to monitor biological processes has gained increased interest from scientists within different research areas, ranging from organic chemistry and photo-physics to biology since its introduction. The technique is generally straightforward and requires only standard equipment, and the result is available within minutes from sample preparation. In this review, the syntheses of oligo and polythiophenes developed over the last decades are discussed. Furthermore, the utilization of these molecular agents for exploring biological events, e.g., DNA hybridization or protein misfolding events, are covered.     

抑癌基因P16在肺癌中的研究进展

抑癌基因P16与细胞周期调控密切相关,其主要作用是参与细胞周期过程,它通过细胞周期与其它癌基因及肿瘤抑制基因相互作用成为正常细胞增殖的调控因子。P16基因主要通过基因缺失、点突变及甲基化而失活,已证实该基因的失活与多种肿瘤的形成与转移密切相关。通过各种分子生物学技术检测出它在肿瘤中的表达,将有助于判断肿瘤的恶性程度、浸润深度及预后,为制定合理的治疗方案提供依据。P16是已知的抑癌基因中唯一通过直接抑制细胞周期而抑制细胞生长的基因,在肿瘤治疗方面有很大的应用前景。P16基因突变在人类恶性肿瘤中普遍存在,因此,有关p16基因的研究已经成为当前分子生物学和分子遗传学研究的重要课题。本文就p16基因的分子生物学特性及它与肺癌的关系作一综述。     

Epigenetic age prediction

Advanced age is the main common risk factor for cancer, cardiovascular disease and neurodegeneration. Yet, more is known about the molecular basis of any of these groups of diseases than the changes that accompany ageing itself. Progress in molecular ageing research was slow because the tools predicting whether someone aged slowly or fast (biological age) were unreliable. To understand ageing as a risk factor for disease and to develop interventions, the molecular ageing field needed a quantitative measure; a clock for biological age. Over the past decade, a number of age predictors utilising DNA methylation have been developed, referred to as epigenetic clocks. While they appear to estimate biological age, it remains unclear whether the methylation changes used to train the clocks are a reflection of other underlying cellular or molecular processes, or whether methylation itself is involved in the ageing process. The precise aspects of ageing that the epigenetic clocks capture remain hidden and seem to vary between predictors. Nonetheless, the use of epigenetic clocks has opened the door towards studying biological ageing quantitatively, and new clocks and applications, such as forensics, appear frequently. In this review, we will discuss the range of epigenetic clocks available, their strengths and weaknesses, and their applicability to various scientific queries.     

Why is it crucial to reintegrate pathology into cancer research?

The integration of pathology with molecular biology is vital if we are to enhance the translational value of cancer research. Pathology represents a bridge between medicine and basic biology, it remains the gold standard for cancer diagnosis, and it plays an important role in discovery studies. In the past, pathology and cancer research were closely associated; however, the molecular biology revolution has shifted the focus of investigators toward the molecular alterations of tumors. The reductionist approach taken in molecular studies is producing great insight into the inner workings of neoplasia, but it can also minimize the importance of histopathology and of understanding the disease as a whole. In turn, pathologists can underestimate the role of molecular studies in developing new ancillary techniques for clinical diagnosis. A multidisciplinary approach that integrates pathology and molecular biology within a translational research system is needed. This process will require overcoming cultural barriers and can be achieved through education, a more effective incorporation of pathology into biological research, and conversely an integration of biological research into the pathology laboratory.     

A systems biology perspective on sVEGFR1: its biological function,pathogenic role and therapeutic use

Angiogenesis is the growth of new capillaries from pre-existent microvasculature. A wide range of pathological conditions, from atherosclerosis to cancer, can be attributed to either excessive or deficient angiogenesis. Central to the physiological regulation of angiogenesis is the vascular endothelial growth factor (VEGF) system – its ligands and receptors (VEGFRs) are thus prime molecular targets of pro-angiogenic and anti-angiogenic therapies. Of growing interest as a prognostic marker and therapeutic target in angiogenesis-dependent diseases is soluble VEGF receptor-1 (sVEGFR1, also known as sFlt-1) – a truncated version of the cell membrane-spanning VEGFR1. For instance, it is known that sVEGFR1 is involved in the endothelial dysfunction characterizing the pregnancy disorder of pre-eclampsia, and sVEGFR1’s therapeutic potential as an anti-angiogenic agent is being evaluated in pre-clinical models of cancer. This mini review begins with an examination of the protein domain structure and biomolecular interactions of sVEGFR1 in relation to the full-length VEGFR1. A synopsis of known and inferred physiological and pathological roles of sVEGFR1 is then given, with emphasis on the utility of computational systems biology models in deciphering the molecular mechanisms by which sVEGFR1’s purported biological functions occur. Finally, we present the need for a systems biology perspective in interpreting circulating VEGF and sVEGFR1 concentrations as surrogate markers of angiogenic status in angiogenesis-dependent diseases.     

Mechanochemical cell biology

Eukaryotic systems self-organise by using molecular railways to shuttle specific sets of molecular components to specific locations. In this way, cells are enabled to become larger, more complex and more varied, subtle and effective in their activities. Because of the fundamental importance of molecular railways in eukaryotic systems, understanding how these railways work is an important research goal. Mechanochemical cell biology is a newly circumscribed subject area that concerns itself with the molecular and cell biological mechanisms of motorised directional transport in living systems.