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BioEssays 12/2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cover Photograph: 3D computer graphics of DNA transcription in eukaryotes. Previously determined molecular structures were placed in this scene according to available experimental data and rendered using the Blender software (). Please see article by Wong, Winn and Mozziconacci . (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Hua Wong, Peter J Winn, Julien Mozziconacci Tags: Cover Picture Source Type: journals

Coming next month:Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Tags: Forthcoming Articles Source Type: journals

Nature of methods in science: technology driven science versus science driven technologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Tags: Correspondence Source Type: journals

The Dictionary of Genomics, Transcriptomics, and ProteomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Miguel A. Andrade-Navarro Tags: Book review Source Type: journals

Transcription-blocking DNA damage in aging: a mechanism for hormesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent evidence from studies on DNA repair systems that are implicated in accelerated aging syndromes, have revealed a mechanism through which low levels of persistent damage might exert beneficial effects for both cancer prevention and longevity assurance. Beneficial effects of adaptive responses to low doses of insults that in higher concentrations show adverse effects are generally referred to as hormesis. There are numerous examples of hormetic effects ranging from mild stresses of irradiation to heat stress, hypergravity, pro-oxidants, or food restriction. Although the notion of hormesis is supported by many observati...
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Björn Schumacher Tags: Problems and paradigms Source Type: journals

Thinking in continua: beyond the "adaptive radiation" metaphorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
"Adaptive radiation" is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making "adaptive radiation" so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the results of these techniques into categorical "adaptive radiation...
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Mark E. Olson, Alfonso Arroyo-Santos Tags: Problems and paradigms Source Type: journals

Thalidomide-induced limb defects: resolving a 50-year-old puzzleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite the recent discovery that thalidomide causes limb defects by targeting highly angiogenic, immature blood vessels, several challenges still remain and new ones have arisen. These include understanding the drug's species specificity, determining molecular target(s) in the endothelial cell, shedding light on the molecular basis of phocomelia and producing a form of the drug that is clinically effective without having side effects. Now that the trigger of thalidomide-induced teratogenesis has been uncovered, a framework is proposed, incorporating and uniting previous models of thalidomide action, explaining how thalido...
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Neil Vargesson Tags: Challenges Source Type: journals

Monoallelic gene expression and mammalian evolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Monoallelic gene expression has played a significant role in the evolution of mammals enabling the expansion of a vast repertoire of olfactory receptor types and providing increased sensitivity and diversity. Monoallelic expression of immune receptor genes has also increased diversity for antigen recognition, while the same mechanism that marks a single allele for preferential rearrangement also provides a distinguishing feature for directing hypermutations. Random monoallelic expression of the X chromosome is necessary to balance gene dosage across sexes. In marsupials only the maternal X chromosome is expressed, while in...
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Barry Keverne Tags: Review articles Source Type: journals

Growth plasticity of the embryonic and fetal heartEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The developing mammalian heart responds to a variety of conditions, including changes in nutrient availability, blood oxygenation, hemodynamics, or tissue homeostasis, with impressive growth plasticity. This ensures the formation of a functional and normal sized organ by birth. During embryonic and fetal development the heart is exposed to various physiological and potentially pathological changes in the intrauterine environment which dramatically impact on normal cardiac function, tissue composition, and morphology. This paper summarizes the mechanisms employed by the embryonic and fetal heart to adapt to various intraute...
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Jörg-Detlef Drenckhahn Tags: Review articles Source Type: journals

RNAi in X inactivation: contrasting findings on the role of interferenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
X inactivation is the process that brings about the dosage equivalence of X-linked genes in females to that of males. This complex process initiated at a very early stage of female embryonic development is orchestrated by long non-coding RNAs transcribed in both sense and antisense orientation. Recent studies present contradicting evidence for the role of small RNAs and RNase III enzyme Dicer in the X inactivation process. In this review, I discuss these results in the overall perspective of X inactivation and gene silencing. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Satya K. Kota Tags: What the papers say Source Type: journals

Sizing up the genomic footprint of endosymbiosisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A flurry of recent publications have challenged consensus views on the tempo and mode of plastid (chloroplast) evolution in eukaryotes and, more generally, the impact of endosymbiosis in the evolution of the nuclear genome. Endosymbiont-to-nucleus gene transfer is an essential component of the transition from endosymbiont to organelle, but the sheer diversity of algal-derived genes in photosynthetic organisms such as diatoms, as well as the existence of genes of putative plastid ancestry in the nuclear genomes of plastid-lacking eukaryotes such as ciliates and choanoflagellates, defy simple explanation. Collectively, these...
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Marek Elias, John M. Archibald Tags: What the papers say Source Type: journals

More than mentoring: the importance of group culture for scientific integrityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Authors: Andrew Moore Tags: Editorial Source Type: journals

Highlights from this IssueEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Tags: Highlights Source Type: journals

BioEssays 12/2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - November 17, 2009 Category: Molecular Biology Tags: Contents Source Type: journals

Dorsal closure in Drosophila: cells cannot get out of the tight spotEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dorsal closure (DC), the closure of a hole in the dorsal epidermis of Drosophila embryos by the joining of opposing epithelial cell sheets, has been used as a model process to study the molecular and cellular mechanisms underlying epithelial spreading and wound healing. Recent studies have provided novel insights into how different tissues function cooperatively in this process. Specifically, they demonstrate a critical function of the epidermis surrounding the hole in modulating the behavior of the amnioserosa cells inside. These findings shed light not only on the mechanisms by which the behavior of different tissues is ...
Source: BioEssays - October 30, 2009 Category: Molecular Biology Authors: Carl-Philipp Heisenberg Source Type: journals

Synthetic cells and organelles: compartmentalization strategiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The recent development of RNA replicating protocells and capsules that enclose complex biosynthetic cascade reactions are encouraging signs that we are gradually getting better at mastering the complexity of biological systems. The road to truly cellular compartments is still very long, but concrete progress is being made. Compartmentalization is a crucial natural methodology to enable control over biological processes occurring within the living cell. In fact, compartmentalization has been considered by some theories to be instrumental in the creation of life. With the advancement of chemical biology, artificial compartme...
Source: BioEssays - October 30, 2009 Category: Molecular Biology Authors: Renée Roodbeen, Jan C. M. van Hest Source Type: journals

A molecular model of chromatin organisation and transcription: how a multi-RNA polymerase II machine transcribes and remodels the [beta]-globin locus during developmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a molecular model of eukaryotic gene transcription. For the [beta]-globin locus, we hypothesise that a transcription machine composed of multiple RNA polymerase II (PolII) assembles using the locus control region as a foundation. Transcription and locus remodelling can be achieved by pulling DNA through this multi-PolII 'reading head'. Once a transcription complex is formed, it may engage an active gene in several rounds of transcription. Observed intergenic sense and antisense transcripts may be the result of PolII pulling the DNA through the reading head whilst searching for the promoter of a gene. Support for...
Source: BioEssays - October 29, 2009 Category: Molecular Biology Authors: Hua Wong, Peter J Winn, Julien Mozziconacci Source Type: journals

Iron metabolism: microbes, mouse, and manEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent advances in research on iron metabolism have revealed the identity of a number of genes, signal transduction pathways, and proteins involved in iron regulation in mammals. The emerging paradigm is a coordination of homeostasis within a network of classical iron metabolic pathways and other cellular processes such as cell differentiation, growth, inflammation, immunity, and a host of physiologic and pathologic conditions. Iron, immunity, and infection are intricately linked and their regulation is fundamental to the survival of mammals. The mutual dependence on iron by the host and invading pathogenic organisms elici...
Source: BioEssays - October 29, 2009 Category: Molecular Biology Authors: Gladys O. Latunde-Dada Source Type: journals

BioEssays 11/2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cover Photograph: Thermal noise is routine in the molecular world. Unsurprisingly, nature has not only adapted to it but found ways for its utilization. Actin polymerization, as well as many other cellular processes, is not a smooth process of lengthening or shortening of actin filaments but a random process vulnerable to thermal fluctuations. Fluctuation-driven subunit exchange between monomeric and polymeric actin pools, also called exchange diffusion, indirectly couples energy of ATP hydrolysis by polymeric actin to the energy of actin polymerization. This provides a basis for regulation of actin filament growth by an a...
Source: BioEssays - October 22, 2009 Category: Molecular Biology Tags: Cover Picture Source Type: journals

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No Abstract. (Source: BioEssays)
Source: BioEssays - October 20, 2009 Category: Molecular Biology Tags: Forthcoming Articles Source Type: journals

Reply to "Humans as second orangutans: sense or nonsense?"Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - October 20, 2009 Category: Molecular Biology Authors: Jeffrey H. Schwartz, John Grehan Tags: Correspondence Source Type: journals

Early steps in plastid evolution: current ideas and controversiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Some nuclear-encoded proteins are imported into higher plant plastids via the endomembrane (EM) system. Compared with multi-protein Toc and Tic translocons required for most plastid protein import, the relatively uncomplicated nature of EM trafficking led to suggestions that it was the original transport mechanism for nuclear-encoded endosymbiont proteins, and critical for the early stages of plastid evolution. Its apparent simplicity disappears, however, when EM transport is considered in light of selective constraints likely encountered during the conversion of stable endosymbionts into fully integrated organelles. From ...
Source: BioEssays - October 20, 2009 Category: Molecular Biology Authors: Andrzej Body[lstrok], Pawe[lstrok] Mackiewicz, John W. Stiller Tags: Problems and paradigms Source Type: journals

Flower symmetry evolution: towards understanding the abominable mystery of angiosperm radiationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Flower symmetry is considered a morphological novelty that contributed significantly to the rapid radiation of the angiosperms, which already puzzled Charles Darwin and prompted him to name this phenomenon an 'abominable mystery'. In 2009, the bicentenary of Darwin's birth and the 150th anniversary of the publication of his seminal work, 'On the Origin of Species', this question can now be more satisfactorily readdressed. Understanding the molecular control of monosymmetry formation in the model species Antirrhinum opened the path for comparative studies with non-model species revealing modifications of this trait. TCP tra...
Source: BioEssays - October 20, 2009 Category: Molecular Biology Authors: Andrea Busch, Sabine Zachgo Tags: Review articles Source Type: journals

The fight for evolution: acceptance through pragmatism?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - October 20, 2009 Category: Molecular Biology Authors: Andrew Moore Tags: Editorial Source Type: journals

Highlights from this IssueEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - October 20, 2009 Category: Molecular Biology Tags: Highlights Source Type: journals

BioEssays 11/2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - October 20, 2009 Category: Molecular Biology Tags: Contents Source Type: journals

Stripe formation in the early fly embryo: principles, models, and networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion is given on frequent network motifs, pointing to spatial stripe formation solutions. (Source: BioEssays)
Source: BioEssays - September 30, 2009 Category: Molecular Biology Authors: Dmitri Papatsenko Source Type: journals

Cancer-associated neochromosomes: a novel mechanism of oncogenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Malignant tumours are often characterised by significant rearrangement of the genome. This may be visible in the form of a deranged karyotype with both loss and gain of DNA sequences extending from chromosomal regions to whole chromosomes. In several tumour types, however, gross genomic derangements are minimal, and tumour cells contain one or more additional (supernumerary) chromosomes that may be unrecognisable in terms of a single origin. In this review we term such chromosomes cancer-associated neochromosomes (CaNCs). In the absence of other identified genomic abnormalities, and because the CaNC is a common feature of ...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Dale W. Garsed, Andrew J. Holloway, David M. Thomas Source Type: journals

Belief versus acceptance: Why do people not believe in evolution?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite being an established and accepted scientific theory for 150 years, repeated public polls show that evolution is not believed by large numbers of people. This essay examines why people do not accept evolution and argues that its poor representation in some science textbooks allows misconceptions, established and reinforced in early childhood, to take hold. There is also a lack of up-to-date examples of evidence for evolution in school textbooks. Poor understanding by science graduates and teachers of the nature of science and incorrect definitions by them of key terminology, serve only to undermine efforts to improv...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: James D. Williams Source Type: journals

The granulin gene family: from cancer to dementiaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The growth factor progranulin (PGRN) regulates cell division, survival, and migration. PGRN is an extracellular glycoprotein bearing multiple copies of the cysteine-rich granulin motif. With PGRN family members in plants and slime mold, it represents one of the most ancient of the extracellular regulatory proteins still extant in modern animals. PRGN has multiple biological roles. It contributes to the regulation of early embryogenesis, to adult tissue repair and inflammation. Elevated PGRN levels often occur in cancers, and PGRN immunotherapy inhibits the growth of hepatic cancer xenografts in mice. Recent studies have de...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Andrew Bateman, Hugh P. J. Bennett Source Type: journals

Plant-microbe symbioses: new insights into common rootsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Arbuscular mycorrhiza (AM), a type of plant-fungal endosymbiosis, and nodulation, a bacterial-plant endosymbiosis, are the most ubiquitous symbioses on earth. Recent findings have established part of a shared genetic basis underlying these interactions. Here, we approach root endosymbioses through the lens of the homology and modularity concepts aiming at further clarifying the proximate and ultimate causes for the establishment of these biological systems. We review the genetics that underlie interspecific signaling and its concomitant shift in genetic programs for either partner. Also, through the comparative analysis of...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Pedro T. Lima, Vitor G. Faria, Pedro Patraquim, Alessandro C. Ramos, José A. Feijó, Élio Sucena Source Type: journals

Circadian and solar clocks interact in seasonal floweringEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The plant maintains a 24-h circadian cycle that controls the sequential activation of many physiological and developmental functions. There is empirical evidence suggesting that two types of circadian rhythms exist. Some plant rhythms appear to be set by the light transition at dawn, and are calibrated to circadian (zeitgeber) time, which is measured from sunrise. Other rhythms are set by both dawn and dusk, and are calibrated to solar time that is measured from mid-day. Rhythms on circadian timing shift seasonally in tandem with the timing of dawn that occurs earlier in summer and later in winter. On the other hand, rhyth...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Hoong-Yeet Yeang Source Type: journals

Fungal incompatibility: Evolutionary origin in pathogen defense?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In fungi, cell fusion between genetically unlike individuals triggers a cell death reaction known as the incompatibility reaction. In Podospora anserina, the genes controlling this process belong to a gene family encoding STAND proteins with an N-terminal cell death effector domain, a central NACHT domain and a C-terminal WD-repeat domain. These incompatibility genes are extremely polymorphic, subject to positive Darwinian selection and display a remarkable genetic plasticity allowing for constant diversification of the WD-repeat domain responsible for recognition of non-self. Remarkably, the architecture of these proteins...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Mathieu Paoletti, Sven J. Saupe Source Type: journals

Catalytic antibodies: balancing between Dr. Jekyll and Mr. HydeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The immunoglobulin molecule is a perfect template for the de novo generation of biocatalytic functions. Catalytic antibodies, or abzymes, obtained by the structural mimicking of enzyme active sites have been shown to catalyze numerous chemical reactions. Natural enzyme analogs for some of these reactions have not yet been found or possibly do not exist at all. Nowadays, the dramatic breakthrough in antibody engineering and expression technologies has promoted a considerable expansion of immunoglobulin's medical applications and is offering abzymes a unique chance to become a promising source of high-precision "catalytic va...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Alexey Belogurov Jr., Arina Kozyr, Natalia Ponomarenko, Alexander Gabibov Source Type: journals

How depolymerization can promote polymerization: the case of actin and profilinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Rapid polymerization and depolymerization of actin filaments in response to extracellular stimuli is required for normal cell motility and development. Profilin is one of the most important actin-binding proteins; it regulates actin polymerization and interacts with many cytoskeletal proteins that link actin to extracellular membrane. The molecular mechanism of profilin has been extensively considered and debated in the literature for over two decades. Here we discuss several accepted hypotheses regarding the mechanism of profilin function as well as new recently emerged possibilities. Thermal noise is routine in molecular...
Source: BioEssays - September 29, 2009 Category: Molecular Biology Authors: Elena G. Yarmola, Michael R. Bubb Source Type: journals

BioEssays 10/2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cover Photograph: A superposition of a fish with colour patterning produced by a gene expression network involving a "paradoxical" relationship between two genes, of the type A inhibits B; B activates A, upon a computer simulation of the same. When explored in terms of spatial resolution, apparent paradoxes represented by simple connectivity diagrams produce undulating patterns; in other situations they produce temporal oscillations. To read more on this topic, see the article by Mark Isalan on pages 1110-1115. Fish image reproduced with kind permission from Anka Zolnierzak; computer simulation image reproduced with kind p...
Source: BioEssays - September 17, 2009 Category: Molecular Biology Tags: Cover Picture Source Type: journals

Coming next month:Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - September 14, 2009 Category: Molecular Biology Tags: Forthcoming Articles Source Type: journals

Humans as second orangutans: sense or nonsense?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - September 14, 2009 Category: Molecular Biology Tags: Commentary Source Type: journals

What we don't know can, and will, hurt usEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - September 14, 2009 Category: Molecular Biology Authors: Andrew Moore Tags: Editorial Source Type: journals

Highlights from this issueEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - September 14, 2009 Category: Molecular Biology Tags: Highlights Source Type: journals

BioEssays 10/2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No Abstract. (Source: BioEssays)
Source: BioEssays - September 14, 2009 Category: Molecular Biology Tags: Contents Source Type: journals

MYST family histone acetyltransferases take center stage in stem cells and developmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Acetylation of histones is an essential element regulating chromatin structure and transcription. MYST (Moz, Ybf2/Sas3, Sas2, Tip60) proteins form the largest family of histone acetyltransferases and are present in all eukaryotes. Surprisingly, until recently this protein family was poorly studied. However, in the last few years there has been a substantial increase in interest in the MYST proteins and a number of key studies have shown that these chromatin modifiers are required for a diverse range of cellular processes, both in health and disease. Translocations affecting MYST histone acetyltransferases can lead to leuke...
Source: BioEssays - September 1, 2009 Category: Molecular Biology Authors: Anne K. Voss, Tim Thomas Source Type: journals

Making the right connections: biological networks in the light of evolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Our understanding of how evolution acts on biological networks remains patchy, as is our knowledge of how that action is best identified, modelled and understood. Starting with network structure and the evolution of protein-protein interaction networks, we briefly survey the ways in which network evolution is being addressed in the fields of systems biology, development and ecology. The approaches highlighted demonstrate a movement away from a focus on network topology towards a more integrated view, placing biological properties centre-stage. We argue that there remains great potential in a closer synergy between evolutio...
Source: BioEssays - August 30, 2009 Category: Molecular Biology Authors: Christopher G. Knight, John W. Pinney Source Type: journals

Gene networks and liar paradoxesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Network motifs are small patterns of connections, found over-represented in gene regulatory networks. An example is the negative feedback loop (e.g. factor A represses itself). This opposes its own state so that when 'on' it tends towards 'off' - and vice versa. Here, we argue that such self-opposition, if considered dimensionlessly, is analogous to the liar paradox: 'This statement is false'. When 'true' it implies 'false' - and vice versa. Such logical constructs have provided philosophical consternation for over 2000 years. Extending the analogy, other network topologies give strikingly varying outputs over different di...
Source: BioEssays - August 30, 2009 Category: Molecular Biology Authors: Mark Isalan Source Type: journals

Identification and targeting of cancer stem cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cancer stem cells (CSC) represent malignant cell subsets in hierarchically organized tumors, which are selectively capable of tumor initiation and self-renewal and give rise to bulk populations of non-tumorigenic cancer cell progeny through differentiation. Robust evidence for the existence of prospectively identifiable CSC among cancer bulk populations has been generated using marker-specific genetic lineage tracking of molecularly defined cancer subpopulations in competitive tumor development models. Moreover, novel mechanisms and relationships have been discovered that link CSC to cancer therapeutic resistance and clini...
Source: BioEssays - August 25, 2009 Category: Molecular Biology Authors: Tobias Schatton, Natasha Y. Frank, Markus H. Frank Source Type: journals

Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein-dominated membranes on their own. In a metabolism-first context, "autocatalytically closed" sets of statistical peptides could organize a self-maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic activities are conside...
Source: BioEssays - August 24, 2009 Category: Molecular Biology Authors: Richard Egel Source Type: journals

Toward general prophylactic cancer vaccinationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It is well established that chronic infections can lead to cancer. Almost unknown is that, in contrast, acute brief viral and bacterial infections may have beneficial effects in cases of established neoplastic disease, while exposure to pathogenic products by infection, vaccination, and inhalation can cause prophylactic effects. In the following I will align evidence from case studies of spontaneous regression and from epidemiological studies with recent immunology to conclude that pathogenic substances belonging to the group of "pathogen-associated molecular patterns" can trigger the innate immune system to establish anti...
Source: BioEssays - August 24, 2009 Category: Molecular Biology Authors: Uwe Hobohm Source Type: journals

Metabolic systems maintain stable non-equilibrium via thermodynamic bufferingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here, we analyze how the set of nucleotides in the cell is equilibrated and how this generates simple rules that help the cell to organize itself via maintenance of a stable non-equilibrium state. A major mechanism operating to achieve this state is thermodynamic buffering via high activities of equilibrating enzymes such as adenylate kinase. Under stable non-equilibrium, the ratios of free and Mg-bound adenylates, Mg2+ and membrane potentials are interdependent and can be computed. The adenylate status is balanced with the levels of reduced and oxidized pyridine nucleotides through regulated uncoupling of the pyridine nuc...
Source: BioEssays - August 24, 2009 Category: Molecular Biology Authors: Abir U. Igamberdiev, Leszek A. Kleczkowski Source Type: journals

RNA editing: a driving force for adaptive evolution?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genetic variability is considered a key to the evolvability of species. The conversion of an adenosine (A) to inosine (I) in primary RNA transcripts can result in an amino acid change in the encoded protein, a change in secondary structure of the RNA, creation or destruction of a splice consensus site, or otherwise alter RNA fate. Substantial transcriptome and proteome variability is generated by A-to-I RNA editing through site-selective post-transcriptional recoding of single nucleotides. We posit that this epigenetic source of phenotypic variation is an unrecognized mechanism of adaptive evolution. The genetic variation ...
Source: BioEssays - August 24, 2009 Category: Molecular Biology Authors: Willemijn M. Gommans, Sean P. Mullen, Stefan Maas Source Type: journals

Changing phosphoinositides "on the fly": how trafficking vesicles avoid an identity crisisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Joining an antagonistic phosphoinositide (PtdInsP) kinase and phosphatase into a single protein complex may regulate rapid and local PtdInsP changes. This may be important for processes such as membrane fission that require a specific PtdInsP and that are innately local and rapid. Such a complex could couple vesicle formation, with erasing of the identity of the donor organelle from the vesicle prior to its fusion with target organelles, thus preventing organelle identity intermixing. Coordinating signals are postulated to switch the relative activities of the kinase and phosphatase in a spatio-temporal manner that matches...
Source: BioEssays - August 24, 2009 Category: Molecular Biology Authors: Roberto J. Botelho Source Type: journals