Mitochondrial introns: a critical view

Although group I and group II introns were discovered more than 25 years ago, they are still difficult to identify. Modeling their RNA structure also remains particularly challenging for organelle sequences, owing to their great diversity. In fact, accelerated evolution in organelles often results in a reduced RNA structure and a loss of autocatalytic splicing and intron mobility. We set out to identify all mitochondrial group I and II introns in published sequences, and, to this end, we developed and applied a new search approach: RNAweasel. On the basis of the results, we focus here on building a comprehensive picture of mitochondrial group I introns, including a modified (reduced) consensus RNA secondary structure and a concise phylogeny-based subclassification.     

Models for chromatin remodeling: a critical comparison.

Nucleosome remodeling has been shown, in many cases, to involve cis displacement of nucleosomes on the DNA. This process seems similar to the long-recognized random diffusion of nucleosomes along DNA, but the remodeling process is unidirectional and ATP dependent. Several years ago, we developed a model for nucleosome migration, based on the diffusion of "twist-defects" within the nucleosomal DNA. This has been modified into a model that incorporates ATP-dependent defect generation, and can account for many observations concerning remodeling. However, certain experimental studies in recent years have cast doubt on the applicability of the twist-diffusion model for remodeling, and seem to favor instead a "reptation" model. We discuss herein these problems and propose a resolution.     

DNA methylation and chromatin structure: a view from below

An understanding of the function and control of DNA methylation in eukaryotes has been elusive. Studies of Neurospora crassa have led to a model that accounts for the chromosomal distribution of methylation and suggests a basic function for DNA methylation in eukaryotes.     

Cohesin: a critical chromatin organizer in mammalian gene regulation

Cohesins are evolutionarily conserved essential multi-protein complexes that are important for higher-order chromatin organization. They play pivotal roles in the maintenance of genome integrity through mitotic chromosome regulation, DNA repair and replication, as well as gene regulation critical for proper development and cellular differentiation. In this review, we will discuss the multifaceted functions of mammalian cohesins and their apparent functional hierarchy in the cell, with particular focus on their actions in gene regulation and their relevance to human developmental disorders.     

Effect of hydrazine deproteination on bone mineral phase: a critical view

Over the last 30 years several techniques have been developed to separate bone matrix and bone mineral, in order to allow for a study of each component independently of the other. Preservation of original characteristics of the phase studied after isolation has always been a great challenge for all such techniques. The hydrazine deproteination procedure, first proposed by Termine, has been one of the processes most widely used for studying bone mineral. It is found to be one of the most effective, notwithstanding controversy over its efficiency in bone deproteination and criticism regarding possible changes it could make to the characteristics of bone mineral. In this work, we have studied the possible chemical and physical alterations caused by the hydrazine deproteination process to bone mineral from rats and to other materials of biological interest. Materials were characterized by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), X-ray diffractometry (XRD), inductive coupled plasma-optical emission spectroscopy (ICP-OES), C-H-N analysis and infrared spectroscopy (FTIR), before and after hydrazine deproteination. Finally, here we present a comprehensive discussion on the criticism of hydrazine deproteination. The experimental results obtained in this work, even when compared to the results in the literature, show that most widespread criticism to the hydrazine deproteination process is not completely justified.     

A critical view on conservative mutations

By analysing the surface composition of a set of protein 3D structures, complemented with predicted surface compositional information for homologous proteins, we have found significant evidence for a layer composition of protein structures. In the innermost and outermost parts of proteins there is a net negative charge, while the middle has a net positive charge. In addition, our findings indicate that the concept of conservative mutation needs substantial revision, e.g. very different spatial preferences were found for glutamic acid and aspartic acid. The alanine screening often used in protein engineering projects involves the substitution of residues to alanine, based on the assumption that alanine is a "neutral" residue. However, alanine has a high negative correlation with all but the non-polar residues. We therefore propose the use of, for example, serine as a substitute for the residues that are negatively correlated with alanine.     

Species-level heritability reaffirmed: a comment on "on the heritability of geographic range sizes"

For many current issues in macroevolution and macroecology, it is important to know to what degree the attributes of species are shared among closely related lineages, a concept sometimes referred to as species-level heritability. Recently, Webb and Gaston proposed a new method for analyzing the heritability of geographic range size and concluded that range size is not heritable in Cretaceous gastropods (data from Jablonski) and modern birds (their data). Here we show that Webb and Gaston's method is flawed in that it implicitly assumes that range sizes are uniformly distributed. When range size distributions show their characteristic strong right skew, Webb and Gaston's method spuriously tends to find that range sizes of closely related pairs of species are more dissimilar than the random expectation. A reanalysis of Jablonski's data finds range size to be robustly and strongly heritable in Cretaceous gastropods and less strongly but still significantly heritable in present-day birds.     

Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time

Wrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non-histone protein-DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA-bound proteins, such as histones or site-specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage-based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single-hit kinetics. Moreover, cleavage-based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase-based, single-molecule MAP-IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP-IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation.     

Hempel's view on functional explanation some critical comments

Summary Functional explanations are regarded as a special type of explanation by many biologists. Philosophers of science tend to agree that they are weak forms of the common modes of explanation, although the elucidation of the logical structure involved is difficult. The present paper shows that Hempel's reconstruction of functional explanations is inadequate on pragmatic grounds. Thus his conclusion that such explanations are necessarily weak is also objectionable. There is no reason for allotting functional explanations a special logical status.     

Stress-induced adrenal changes and their relation to reproductive failure in captive nine-banded armadillos (Dasypus novemcinctus)

Histological features of adrenal glands from captive and unstressed free-ranging nine-banded armadillos were compared to determine if undefined stress factors associated with captivity were capable of causing changes in adrenal morphology. Animals in captivity less than 3 mo showed histological features identical to unstressed free-ranging animals. Animals in captivity 6 mo or longer, however, showed adrenal changes like those previously described in other mammals exposed to various types of stress, except that there was no accompanying increase in adrenal weight. Similar adrenal changes were found in free-ranging animals exposed to extremely harsh winter weather. Females from both the chronic captive population and this stressed free-ranging population were seen to suffer reproductive failure. Reproductive function in males was not affected. There was no detectable sex difference in gross or histological adrenal changes; however, previous reports indicate there is a sex difference in the secretory product from the adrenals of captive nine-banded armadillos. A possible relationship between reproductive failure in the female and the sex difference in adrenal secretory products is discussed.     

Stem cell research in Asia: A critical view

Stem cell research stands as a high‐priority field in many countries across the Asia‐Pacific region, and the past decade has seen remarkable investment into facilities and programs intended to increase competitiveness in the drive to find clinical applications. In the years roughly framed by Korean cloner Woo‐Suk Hwang's meteoric ascent and fall, speculation was rampant that Asia was poised to overtake the West in this field of science. But that potential remains unfulfilled. In this article, I will look at some of the deficits in infrastructure and governance that underlie the East–West stem cell gap, and suggest a number of measures that might be taken to remedy them. J. Cell. Biochem. 107: 853–856, 2009. © 2009 Wiley‐Liss, Inc.     

Stress-induced Antibiotic Susceptibility Testing on a Chip

We have developed a rapid microfluidic method for antibiotic susceptibility testing in a stress-based environment. Fluid is passed at high speeds over bacteria immobilized on the bottom of a microfluidic channel. In the presence of stress and antibiotic, susceptible strains of bacteria die rapidly. However, resistant bacteria survive these stressful conditions. The hypothesis behind this method is new: stress activation of biochemical pathways, which are targets of antibiotics, can accelerate antibiotic susceptibility testing. As compared to standard antibiotic susceptibility testing methods, the rate-limiting step - bacterial growth - is omitted during antibiotic application. The technical implementation of the method is in a combination of standard techniques and innovative approaches. The standard parts of the method include bacterial culture protocols, defining microfluidic channels in polydimethylsiloxane (PDMS), cell viability monitoring with fluorescence, and batch image processing for bacteria counting. Innovative parts of the method are in the use of culture media flow for mechanical stress application, use of enzymes to damage but not kill the bacteria, and use of microarray substrates for bacterial attachment. The developed platform can be used in antibiotic and nonantibiotic related drug development and testing. As compared to the standard bacterial suspension experiments, the effect of the drug can be turned on and off repeatedly over controlled time periods. Repetitive observation of the same bacterial population is possible over the course of the same experiment.     

Stress-induced changes of circulating neuropeptide Y in the rat: comparison with catecholamines

Circulating concentrations of neuropeptide Y-like immunoreactivity (NPY), noradrenaline (NA) and adrenaline (AD) were measured in conscious, chronically catheterized rats submitted to various stress protocols. Basal plasma levels of NPY, NA and AD (194 +/- 52 fmol/ml, 0.90 +/- 0.11 pmol/ml and 0.52 +/- 0.07 pmol/ml) were increased by handling (+132%, +76% and +629%, respectively) and rose further during electric shock treatment. Adrenalectomy resulted in the complete disappearance of circulating adrenaline but did not alter either control or stress values of noradrenaline. In comparison circulating levels of NPY were reduced, but not significantly in adrenalectomized animals. Insulin stress induced a large increase in plasma AD levels and cold stress induced an increase in plasma NA levels, without any parallel change in NPY concentrations. These results demonstrate that NPY, which is colocalized with catecholamines in the peripheral nervous systems, is also released during stress responses and that its release parallels more closely changes in circulating NA than AD. Furthermore, stress-induced changes in circulating NPY-like immunoreactivity do not originate from the adrenal gland but mainly from the peripheral nervous system, and the release of NPY is dependent upon the nature of the stimulus.     

Tumor initiating cells in pancreatic cancer: A critical view

Emerging evidence points to the existence of pancreatic cancer stem cells (CSC) as the culprit in the initiation, maintenance, metastasis, and treatment resistance of pancreatic cancer. The existence of such a cell population would have an important impact on the design of novel therapies against this devastating disease. However, no in vivo validation or rebuttal of the pancreatic CSC hypothesis exists. Major backlashes in the discussion on CSC are firstly, the confusion between the terms CSC and cell of origin of pancreatic ductal adenocarcinoma (PDAC), secondly the ambiguity of the cell of origin itself and thirdly, the fact that the CSC hypothesis is based on cell sorting and xenografting experiments; the latter of which often precludes solid conclusions because of the lack of a natural microenvironment and differences in drug delivery. Nonetheless, recent studies in other cancers partially support the CSC hypothesis by demonstrating a link between epithelial-to-mesenchymal transdifferentiation/transition (EMT) and CSC properties. Such a link is again open to dispute as EMT is a reversible process which is highly dependent on major oncogenic pathways in PDAC [e.g. K-Ras, transforming growth factor-β (TGF-β)] rather than on presumed cancer stem cell pathways. Hence, the available evidence does not robustly support the CSC concept in PDAC and a thorough validation of this hypothesis in well-defined genetically engineered mouse models of pancreatic cancer is required.