The structure and assembly of active chromatin

Much effort has been expended towards understanding the details of how nucleosomes are established on newly replicated DNA. More recently it has begun to be possible to study the binding of both trans-acting factors and histones to DNA. This review is concerned with an assessment of the current status of this work. In addition, we discuss some of the questions that still need to be addressed in order to understand how trans-acting factors can establish extensive interactions with the DNA of active genes while they are excluded from inactive genes.     

Studies on bleomycin-DNA and bleomycin-iron interactions

The bleomycins, a group of antitumor antibiotics (Figure 1), cause the degradation of DNA by a process requiring iron(II) and dioxygen (1,2). DNA degradation appears to involve two steps: association of the drug with the nucleic acid and degradation of the DNA. As part of studies directed toward achieving an understanding of how the bleomycins degrade DNA, we have examined various properties of the drug using a variety of chemical and physico-chemical techniques, including NMR and M?ssbauer spectroscopy. We have studied both the interaction of the antibiotic with its target (DNA) as well as its association with its metal ion cofactor. This work has been performed on the intact drug and its derivatives as well as on synthetic models of the parent drug. This paper reviews and updates the recent work from this laboratory on the bleomycins.     

Modeling for Understanding v. Modeling for Numbers

I draw a distinction between Modeling for Numbers, which aims to address how much, when, and where questions, and Modeling for Understanding, which aims to address how and why questions. For-numbers models are often empirical, which can be more accurate than their mechanistic analogues as long as they are well calibrated and predictions are made within the domain of the calibration data. To extrapolate beyond the domain of available system-level data, for-numbers models should be mechanistic, relying on the ability to calibrate to the system components even if it is not possible to calibrate to the system itself. However, development of a mechanistic model that is reliable depends on an adequate understanding of the system. This understanding is best advanced using a for-understanding modeling approach. To address how and why questions, for-understanding models have to be mechanistic. The best of these for-understanding models are focused on specific questions, stripped of extraneous detail, and elegantly simple. Once the mechanisms are well understood, one can then decide if the benefits of incorporating the mechanism in a for-numbers model is worth the added complexity and the uncertainty associated with estimating the additional model parameters.     

Do the same traffic rules apply? Directional chromosome segregation by SpoIIIE and FtsK

Over a decade of studies have tackled the question of how FtsK/SpoIIIE translocases establish and maintain directional DNA translocation during chromosome segregation in bacteria. FtsK/SpoIIIE translocases move DNA in a highly processive, directional manner, where directionality is facilitated by sequences on the substrate DNA molecules that are being transported. In recent years, structural, biochemical, single‐molecule and high‐resolution microscopic studies have provided new insight into the mechanistic details of directional DNA segregation. Out of this body of work, a series of models have emerged and, ultimately, yielded two seemingly opposing models: the loading model and the target search model. We review these recent mechanistic insights into directional DNA movement and discuss the data that may serve to unite these suggested models, as well as propose future directions that may ultimately solve the debate.     

Epigenetic variation and inheritance in mammals

What determines phenotype is one of the most fundamental questions in biology. Historically, the search for answers had focused on genetic or environmental variants, but recent studies in epigenetics have revealed a third mechanism that can influence phenotypic outcomes, even in the absence of genetic or environmental heterogeneity. Even more surprisingly, some epigenetic variants, or epialleles, can be inherited by the offspring, indicating the existence of a mechanism for biological heredity that is not based on DNA sequence. Recent work from mouse models, human monozygotic twin studies, and large-scale epigenetic profiling suggests that epigenetically determined phenotypes and epigenetic inheritance are more common than previously appreciated.     

Lipid metabolism in skeletal muscle: generation of adaptive and maladaptive intracellular signals for cellular function

Fatty acids derived from adipose tissue lipolysis, intramyocellular triacylglycerol lipolysis, or de novo lipogenesis serve a variety of functions in skeletal muscle. The two major fates of fatty acids are mitochondrial oxidation to provide energy for the myocyte and storage within a variety of lipids, where they are stored primarily in discrete lipid droplets or serve as important structural components of membranes. In this review, we provide a brief overview of skeletal muscle fatty acid metabolism and highlight recent notable advances in the field. We then 1) discuss how lipids are stored in and mobilized from various subcellular locations to provide adaptive or maladaptive signals in the myocyte and 2) outline how lipid metabolites or metabolic byproducts derived from the actions of triacylglycerol metabolism or β-oxidation act as positive and negative regulators of insulin action. We have placed an emphasis on recent developments in the lipid biology field with respect to understanding skeletal muscle physiology and discuss unanswered questions and technical limitations for assessing lipid signaling in skeletal muscle.     

Quality control compartments coming of age

Maintenance of proteome integrity (proteostasis) is essential for cellular and organismal survival. Various cellular mechanisms work to preserve proteostasis by ensuring correct protein maturation and efficient degradation of misfolded and damaged proteins. Despite this cellular effort, under certain circumstances subsets of aggregation-prone proteins escape the quality control surveillance, accumulate within the cell and form insoluble aggregates that can lead to the development of disorders including late-onset neurodegenerative diseases. Cells respond to the appearance of insoluble aggregates by actively transporting them to designated deposition sites where they often undergo degradation. Although several protein aggregate deposition sites have been described and extensively studied, key questions regarding their biological roles and how they are affected by aging remained unanswered. Here we review the recent advances in the field, describe the different subtypes of these cellular compartments and outline the evidence that these structures change their properties over time. Finally, we propose models to explain the possible mechanistic links between aggregate deposition sites, neurodegenerative disorders and the aging process.     

Neurocognitive insights on conceptual knowledge and its breakdown

Conceptual knowledge reflects our multi-modal ‘semantic database’. As such, it brings meaning to all verbal and non-verbal stimuli, is the foundation for verbal and non-verbal expression and provides the basis for computing appropriate semantic generalizations. Multiple disciplines (e.g. philosophy, cognitive science, cognitive neuroscience and behavioural neurology) have striven to answer the questions of how concepts are formed, how they are represented in the brain and how they break down differentially in various neurological patient groups. A long-standing and prominent hypothesis is that concepts are distilled from our multi-modal verbal and non-verbal experience such that sensation in one modality (e.g. the smell of an apple) not only activates the intramodality long-term knowledge, but also reactivates the relevant intermodality information about that item (i.e. all the things you know about and can do with an apple). This multi-modal view of conceptualization fits with contemporary functional neuroimaging studies that observe systematic variation of activation across different modality-specific association regions dependent on the conceptual category or type of information. A second vein of interdisciplinary work argues, however, that even a smorgasbord of multi-modal features is insufficient to build coherent, generalizable concepts. Instead, an additional process or intermediate representation is required. Recent multidisciplinary work, which combines neuropsychology, neuroscience and computational models, offers evidence that conceptualization follows from a combination of modality-specific sources of information plus a transmodal ‘hub’ representational system that is supported primarily by regions within the anterior temporal lobe, bilaterally.     

Studies on Bleomycin-DNA and Bleomycin-Iron Interactions

Abstract

The bleomycins, a group of antitumor antibiotics (Figure 1), cause the degradation of DNA by a process requiring iron(II) and dioxygen (1,2). DNA degradation appears to involve two steps: association of the drug with the nucleic acid and degradation of the DNA. As part of studies directed toward achieving an understanding of how the bleomycins degrade DNA, we have examined various properties of the drug using a variety of chemical and physico- chemical techniques, including NMR and Mössbauer spectroscopy. We have studied both the interaction of the antibiotic with its target (DNA) as well as its association with its metal ion cofactor. This work has been performed on the intact drug and its derivatives as well as on synthetic models of the parent drug. This paper reviews and updates the recent work from this laboratory on the bleomycins.     

The evolution of noncoding DNA: how much junk, how much func?

Comparative sequence analysis on a genomic scale has opened the door for the systematic analysis of cis-acting regulatory DNA. It is now possible to begin to answer basic questions such as, how much meaningful noncoding sequence is in the genome? How strong is natural selection on functional noncoding sequences in different species? Two recent articles have capitalized on the comparative genomic approach in an attempt to answer these questions with surprising results.     

In vivo divisional tracking of hematopoietic stem cells

Hematopoietic stem cell (HSC) division leads to self-renewal, differentiation, or death of HSCs, and adequate balance of this process results in sustained, lifelong, high-throughput hematopoiesis. Despite their contribution to hematopoietic cell production, the majority of cells within the HSC population are quiescent at any given time. Recent studies have tackled the questions of how often HSCs divide, how divisional history relates to repopulating potential, and how many HSCs contribute to hematopoiesis. Here, we summarize these recent findings on HSC turnover from different experimental systems and discuss hypothetical models for HSC cycling and maintenance in steady-state and upon hematopoietic challenge.     

Synthetic cell biology

Synthesis of data into formal models of cellular function is rapidly becoming a necessary industry. The complexity of the interactions among cellular constituents and the quantity of data about these interactions hinders the ability to predict how cells will respond to perturbation and how they can be engineered for industrial or medical purposes. Models provide a systematic framework to describe and analyze these complex systems. In the past few years, models have begun to have an impact on mainstream biology by creating deeper insight into the design rules of cellular signal processing, providing a basis for rational engineering of cells, and for resolving debates about the root causes of certain cellular behaviors. This review covers some of the recent work and challenges in developing these "synthetic cell" models and their growing practical applications.     

Tinkering with transporters: Periplasmic binding protein-dependent maltose transport inE. coli

Periplasmic binding protein-dependent transport systems represent a common mechanism for nutrient and ion uptake in bacteria. As a group, these systems are related to one another and to other transporters of both prokaryotes and eukaryotes, based on sequence similarity within an ATP-binding subunit and overall structural organization. These transporters probably all use energy derived from ATP to pump substrates across membranes. Although there is considerable information about the sequences and identity of the transporters, there is little information about how they work. That is, where do ligands bind? Where do the subunits or domains interact with one another? How is the energy of nucleotide binding and/or hydrolysis converted to conformational changes? In order to address these questions we have taken a genetic approach that involves studying mutant forms of a transporter. Rather than study mutations that result in complete loss of function, the study of mutations which perturb or alter the normal function of the transporter in a defined manner has provided a limited insight into how the answers to these questions may be obtained.     

The impact of next-generation sequencing technology on genetics

If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism.     

Histone marks: repairing DNA breaks within the context of chromatin

Inherited or acquired defects in detecting, signalling or repairing DNA damage are associated with various human pathologies, including immunodeficiencies, neurodegenerative diseases and various forms of cancer. Nuclear DNA is packaged into chromatin and therefore the true in vivo substrate of damaged DNA occurs within the context of chromatin. Our work aims to decipher the mechanisms by which cells detect DNA damage and signal its presence to the DNA-repair and cell-cycle machineries. In particular, much of our work has focused on DNA DSBs (double-strand breaks) that are generated by ionizing radiation and radiomimetic chemicals, and which can also arise when the DNA replication apparatus encounters other DNA lesions. In the present review, we describe some of our recent work, as well as the work of other laboratories, that has identified new chromatin proteins that mediate DSB responses, control SDB processing or modulate chromatin structure at DNA-damage sites. We also aim to survey several recent advances in the field that have contributed to our understanding of how particular histone modifications and involved in DNA repair. It is our hope that by understanding the role of chromatin and its modifications in promoting DNA repair and genome stability, this knowledge will provide opportunities for developing novel classes of drugs to treat human diseases, including cancer.     

<Emphasis Type="Italic">Drosophila</Emphasis> as models to understand the adaptive process during invasion

The last few decades have seen a growing number of species invasions globally, including many insect species. In drosophilids, there are several examples of successful invasions, i.e. Zaprionus indianus and Drosophila subobscura some decades ago, but the most recent and prominent example is the invasion of Europe and North America by the pest species, Drosophila suzukii. During the invasive process, species often encounter diverse environmental conditions that they must respond to, either through rapid genetic adaptive shifts or phenotypic plasticity, or by some combination of both. Consequently, invasive species constitute powerful models for investigating various questions related to the adaptive processes that underpin successful invasions. In this paper, we highlight how Drosophila have been and remain a valuable model group for understanding these underlying adaptive processes, and how they enable insight into key questions in invasion biology, including how quickly adaptive responses can occur when species are faced with new environmental conditions.