Base Compositional Bias and Phylogenetic Analyses: A Test of the “Flying DNA” Hypothesis

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994,Curr. Biol.4:277–280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's “flying DNA” hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the “flying DNA” hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.     

Flexibility versus “rigidity” of the functional architecture of AChE active center

Functional architecture of the AChE active center appears to be characterized by both structural “rigidity”, necessary to stabilize the catalytic triad as well as by flexibility in accommodating the different, high affinity AChE ligands. These seemingly conflicting structural properties of the active center are demonstrated through combination of structural methods with kinetic studies of the enzyme and its mutant derivatives with plethora of structurally diverse ligands and in particular with series of stereoselective covalent and noncovalent AChE ligands. Thus, steric perturbation of the acyl pocket precipitates in a pronounced stereoselectivity toward methylphosphonates by disrupting the stabilizing environment of the catalytic histidine rather than through steric exclusion demonstrating the functional importance of the “rigid” environment of the catalytic machinery. The acyl pocket, the cation-binding subsite (Trp86) and the peripheral anionic subsite were also found to be directly involved in HuAChE stereoselectivity toward charged chiral phosphonates, operating through differential positioning of the ligand cationic moiety within the active center. Residue Trp86 is also a part of the “hydrophobic patch” which seems flexible enough to accommodate the structurally diverse ligands like tacrine, galanthamine and the two diastereomers of huperzine A. Also, we have recently discovered further aspects of the role of both the unique structure and the flexibility of the “hydrophobic patch” in determining the reactivity and stereoselectivity of HuAChE toward certain carbamates including analogs of physostigmine. In these cases the ligands are accommodated mostly through hydrophobic interactions and their stereoselectivity delineates precisely the steric limits of the pocket. Hence, the HuAChE stereoselectivity provides a sensitive tool in the in depth exploration of the functional architecture of the active center. These studies suggest that the combination of “rigidity” and flexibility within the HuAChE gorge are an essential element of its molecular design.     

“Advanced Voice Function Assessment”—Goals and activities of COST Action 2103

The COST Action 2103 “Advanced Voice Function Assessment” is a joint initiative of speech processing teams (engineers and physicists) and the European Laryngological Research Group (ELRG) (laryngologists/phoniatricians). The Action officially started in December 2006, and is running till the end of 2010. 17 European countries are involved. A main objective is a better understanding of the relationship between biomechanical changes at the level of the vocal folds – as induced by pathology and tissue reaction to strain – and alterations of the acoustical voice signal. This needs to result in developing accurate, objective and clinically useful methods of investigation of voice quality in patients, and of strategies for preventing occupational voice disorders in professional speakers. Modelling is an essential tool in this process.     

The development of a “microtitre” fluctuation test for the detection of indirect mutagens, and its use in the evaluation of mixed enzyme induction of the liver

The “Microtitre” Fluctuation test recently introduced for the detection of direct mutagens has been adapted for the detection of indirect mutagens through the incorporation of an “S9-mix” metabolic system. It compares favourably with Greens' original method for the detection of a range of chemical mutagens.

The technique has been employed in the evaluation of mixed enzyme induction using phenobarbitone and β-naphthoflavone (benzoflavone). as a safe substitute for Aroclor-1254. The post-mitochondrial preparations from rats induced with the combined inducers had a similar “metabolic competence” to those derived from Aroclor induced animals. Such a combination would therefore provide a useful alternative to Aroclor-1254 for routine screening.

It was found that the level of “S9” present in the metabolic system greatly affected the quantitative mutagenic response. This varied considerably from chemical to chemical and underlined the need for such preliminary investigations in routine screening.     

Hong Kong’s worst “red tide”—causative factors reflected in a phytoplankton study at Port Shelter station in 1998

From March through April 1998, a massive “red tide” occurred in coastal waters of south China, including Hong Kong. The “red tide” rapidly killed various species of caged fish and affected coral fishes, killing a few of them, and caused great economic loss and ecological damage. Samples collected from a permanent station located in Port Shelter revealed a new dinoflagellate species, Karenia digitata which was suspected to be the causative species of this “red tide”. Species composition and abundance analysis revealed that an algal bloom persisted in Port Shelter during this entire period. Diatoms and dinoflagellates were the two main groups which dominated the phytoplankton and, in general, when there was an increase in the density of diatoms there was a decline in the density of dinoflagellates, and vice versa. The suspected “red tide” causative species together with other dinoflagellate species started to bloom in late February and reached their highest density on 18 March, when fish kills were first reported at Crooked Island, a semi-enclosed bay to the northeast of Hong Kong. During a 16-week period, dinoflagellate species dominated three times, and coincided with low wind speeds. Constant salinity and a continuing increase in sea surface water temperature suggested warm water intrusion into Hong Kong’s coastal waters during this “red tide” bloom period. Various nutrient elements, e.g. NH₄-N, total Kjeldahl nitrogen (TKN), and PO₄-P were high at the beginning of the bloom but experienced a sharp decrease thereafter. It is suggested that this early 1998 massive “red tide” in Hong Kong waters might have been triggered by a synchronous appearance of optimal climatic, nutritional and hydrographic conditions.     

Floral abnormalities in field grown “Tigrina” plants from xHaynaldoticum sardoum Meletti et Onnis (Gramineae)

A ‘tigrina’ mutant stock of xHaynaldoticum sardoum Meletti et Onnis grown under field conditions produced high frequency spikes with abnormal stamens and pistils. The abnormalities occurred mostly in the stamens, which frequently changed to either pseudoovaries, or leaf-shaped structures or, in extreme cases, did not form at all. The developmental abnormalities of the stamens resulted in male sterility in the whole or in part of the spike. It is proposed that the “tigrina” status changes the physiology of the plant (e.g. photosynthetic activity) in such a way that it responds with floral abnormalities brought about by environmental conditions which permit normal flower development in control (non-mutant) plants.     

Glucose biosensor based on nano-SiO2 and “unprotected” Pt nanoclusters

The “unprotected” Pt nanoclusters (average size 2 nm) mixed with the nanoscale SiO₂ particles (average size 13 nm) were used as a glucose oxidase immobilization carrier to fabricate the amperometric glucose biosensor. The bioactivity of glucose oxidase (GOx) immobilized on the composite was maintained and the as-prepared biosensor demonstrated high sensitivity (3.85 μA mM⁻¹) and good stability in glucose solution. The Pt–SiO₂ biosensor showed a detection limit of 1.5 μM with a linear range from 0.27 to 4.08 mM. In addition, the biosensor can be operated under wide pH range (pH 4.9–7.5) without great changes in its sensitivity. Cyclic voltammetry measurements showed a mixed controlled electrode reaction.     

“Harpoon” Model for Cell–Cell Adhesion and Recognition of Target Cells by the Natural Killer Cells

The mechanism of recognition by natural killer (NK) cells is still unknown. A dynamic model is formulated describing recognition or NK-sensitive target cells (TCs) by NK cells of NK-like cells. This model does not assume the presence of the specific NK-receptor(s) on the membrane of NK cells and corresponding specific ligands on the NK-sensitive TCs. We suggest: (1) the expression of various kinds of “non-NK receptors” and corresponding ligands (counter-receptors) on the plasma membrane of the same NK cell and, possibly, of TCs (e.g. LFA-1 and ICAM-1-ICAM3, CD2 and LFA-3; receptors for TNF and corresponding ligand etc.); (2) the presence of multiple disorders in the organization of “extracellular matrix-surface membrane-submembrane cytoskeleton” assembly of the NK-sensitive TCs; (3) non-specific primary linking of NK cell with TCs, which induces a transfer of vesicles or membrane fragments from the NK surface to the target cell surface (and perhaps vice versa). These processes may also permit the transfer of many types of receptor and counter-receptor molecules from the surface of one conjugated cell to another by vesicles or membrane fragments. After transferral through the intercellular cleft, the free receptors and counter-receptors will be localized on both cell surfaces at the contact region between conjugated cells. By this model the NK cell can “harpoon” the TC and enhance the binding forces between cells up to the critical level and then switch on killing mechanisms for the TC. By means of this “harpoon” model of cell recognition, it seems possible to explain the nature of the wide polymorphism of TCs which are sensitive to the effect of NK and NK-like cells. A mathematical model of the NK cell cytotoxic reaction is described. The model describes many nonlinear peculiarities of the cytotoxic process and predicts some new phenomena. We suggest new approaches of manipulation of cell membranes which can transform NK-resistant target cells in NK sensitive cells and vice versa.     

“Action potentials” in NEUROSPORA CRASSA, a mycelial fungus

Occasional spontaneous “action potentiais” are found in mature hyphae of the fungus Neurospora crassa. They can arise either from low-level sinusoidal oscillations of the membrane potential or from a linear slow depolarization which accelerates into a rapid upstroke at a voltage 5–20 mV depolarized from the normal resting potential (near − 180 mV). The “action potentiais” are long-lasting, 1–2 min and at the peak reach a membrane potential near −40 mV. A 2− to 8−fold increase of membrane conductance accompanies the main depolarization, but a slight decrease of membrane conductance occurs during the slow depolarization. Two plausible mechanisms for the phenomenon are (a) periodic increases of membrane permeability to inorganic ions, particularly H⁺ or Cl^- and (b) periodic decreases in activity of the major electrogenic pump (H⁺) of the Neurospora membrane, coupled with a nonlinear (inverse sigmoid) current-voltage relationship.Identification of action potential-like disturbances in fungi means that such behavior has now been found in all major biologic taxa which have been probed with suitable electrodes. As yet there is no obvious function for the events in fungi.     

Electromigration methods for amino acids, biogenic amines and aromatic amines

Methods of electromigration in laboratory apparatus of small-bore size have recently undergone development at a remarkably rapid pace, leading to a variety of new analytical techniques. One such technique is called “capillary electrophoresis” (CE), which is further classified on the basis of electromigration mode, viz., “capillary zone electrophoresis” (CZE), which, in turn, has several variations. This review aims to give a short overview of the various electromigration methods for amino compounds by using CE. Firstly, this review briefly summarizes the detection methods employed for detection of monoamines and polyamines by CE for both native and derivative forms. Next, current CE methods are described, and their applications to detection of amino acids, biogenic amines, aromatic amines, including heteroaromatic amines and their enantiomers, are introduced from representative papers. Finally, new methods for single-cell analysis and microchip CE techniques are focused on.     

Antagonistic effect of enterocin CCM 4231 from Enterococcus faecium on “bryndza”, a traditional Slovak dairy product from sheep milk

“Bryndza” is a traditional Slovak dairy product (type of soft cheese) made from sheep cheese which was ripened for 14 days. Because its manufacture, transporting and/or storing represent conditions which facilitate contamination, the effect of enterocin CCM4231 in “bryndza” was investigated with the aim to reduce the contaminant agents. “Bryndza” was divided into equal portions (50 g). The experimental sample (ES) as well as the control sample one (C1) were inoculated with Listeria innocua Li1 strain. The other control samples C2 and C3 were without Li1 strain. C3 control was selected as a reference control. ES and C2 portions were treated with purified enterocin CCM4231 in a concentration of 6400 AU/ml. Before the experimental inoculation, “bryndza” was checked for the presence of contaminant agents. The experiment lasted 1 week and the samples were stored in the refrigerator at 4 °C. Sampling was performed on day 1, on day 4 and on day 7. The control samples C2 and C3 were checked only on day 1 and then after 1 week. The following contaminant agents were detected in “bryndza” before its experimental inoculation with L. innocua Li1 strain: Escherichia coli in the amount 10³ cfu/ml/g, Staphylococcus aureus (10² cfu/ml/g) and enterococci (10⁴ cfu/ml/g). In the control sample C2, the number of E. coli was reduced to 10² cfu/ml/g. Enterococci and staphylococci were totally eliminated there. Concerning C3 control, natural decrease of bacteria was found and/or their unchanged counts. The value of pH (5) was stable during the whole experiment. In the experimental sample inoculated with Li1 strain, its counts were decreased immediately after enterocin CCM4231 addition approximately by one order of magnitude. This inhibitory effect was also detectable on day 4 by the difference of one order of magnitude between ES and C1. On day 7, 10³ cfu/ml/g of Li1 strain were detected in both samples (ES, C1). The difference by one order of magnitude indicated, an inhibitory effect of enterocin CCM4231 in “bryndza”. However, bacteriocin activity was not determined by laboratory analyses.     

Cellular “bauplans”: Evolving unicellular forms by means of Julia sets and Pickover biomorphs

The universe of cellular forms has received scarce attention by mainstream neo-Darwinian views. The possibility that a fundamental trait of biological order may consist upon, or be guided by, developmental processes not completely amenable to natural selection was more akin to previous epochs of biological thought, i.e. the “bauplan” discussion. Thirty years ago, however, Lynn and Tucker studied the biological mechanisms responsible for defining organelles position inside cells. The fact that differentiated structures performing a specific function within the eukaryotic cell (i.e. mitochondrion, vacuole, or chloroplast) were occupying specific positions in the protoplasm was the observational and experimental support of the ‘morphogenetic field’ notion at the cellular level. In the present paper we study the morphogenetic field evolution yielding from an initial population of undifferentiated cells to diversified unicellular organisms as well as specialized eukaryotic cell types. The cells are represented as Julia sets and Pickover biomorphs, simulating the effect of Darwinian natural selection with a simple genetic algorithm. The morphogenetic field “defines” the locations where cells are differentiated or sub-cellular components (or organelles) become organized. It may be realized by different possibilities, one of them by diffusing chemicals along the Turing model. We found that Pickover cells show a higher diversity of size and form than those populations evolved as Julia sets. Another novelty is the way that cellular organelles and cell nucleus fill in the cell, always in dependence on the previous cell definition as Julia set or Pickover biomorph. Our findings support the existence of specific attractors representing the functional and stable form of a differentiated cell—genuine cellular bauplans. The configuration of the morphogenetic field is “attracted” towards one or another attractor depending on the environmental influences as modeled by a particular fitness function. The model promotes the classical discussions of D’Arcy Thompson and the more recent views of Waddington, Goodwin and others that consider organisms as dynamical systems that evolve through a ‘master plan’ of transformations, amenable to natural selection. Intriguingly, the model also connects with current developments on mechanobiology, highlighting the informational–developmental role that cytoskeletons may play.     

The emerging role of ICP-MS in proteomic analysis

Quantitative proteomics and absolute determination of proteins are topics of fast growing interest, since only the quantity of proteins or changes in their abundance reflect the status and extent of changes of a given biological system. Quantification of the desired proteins has been carried out by molecule specific MS techniques, but relative quantifications are commonplace so far even resorting to stable isotope labelling techniques such as ICAT and SILAC. In the last decade the idea of using element-selective mass spectrometric detection (e.g. ICP-MS instruments) to achieve absolute quantification has been realised and ICP-MS stands now as a new tool in the field of quantitative proteomics.In this review the emerging role of ICP-MS in protein and proteomic analysis is highlighted. The potential of ICP-MS methods and strategies for screening multiple heteroatoms (e.g. S, P, Se, metals) in proteins and their mixtures and extraordinary capabilities to tackle the problem of absolute protein quantifications, via heteroatom determinations, are discussed and illustrated. New avenues are also open derived from the use of ICP-MS for precise isotope abundance measurements in polyisotopic heteroatoms. The “heteroatom (isotope)-tagged proteomics” concept is focused on the use of naturally present element tags and also extended to any protein by resorting to bioconjugation reactions (i.e. labelling sought proteins and peptides with ICP-MS detectable heteroatoms). A major point of this review is displaying the possibilities of using a “hard” ion source, the ICP, to complement well-established “soft” ion sources for mass spectrometry to tackle present proteomic analysis.     

The efficacy of the extraovular “Prostaglandin-Impact” in provoking first trimester abortion

In good agreement with earlier findings (1–8) legal abortion had been induced successfully with Csapo's method of “Prostaglandin Impact” (PGI) in 44 out of 50 sedated patients. They were 25±1.1 years of age, 11.3±0.2 weeks pregnant, para 1.1±0.2. Only a PGI (10 mg PG F2α) was delivered into the extraovular space. In 44 women, this single PGI provoked 40% progesterone (P)-withdrawal in 3 hours (P < 0.001) and 64% P-withdrawal (P < 0.001) in 15.3±0.9 hours, when the patients aborted. The remaining 6 women, whose P-withdrawal was only 14% at 3 hours without continuation during 24 hours, failed to abort. Thus in PG-induced abortions the regulatory significance of rapid and continued P-withdrawal (1–8) had been verified.The side effects were mild, transient and acceptable. The “Abortion Score” was 86. There were no serious complaints or complications during the study and followup. Since even in the 6 cases of failure the cervix dilated sufficiently to allow curettage (without surgical dilatation), the therapeutic benefits of the single PGI technique should be further examined in those services, where constant medical supervision (for determining the necessity and timing of repeated PGI) is not available.     

Differential staining of chromatids reveals substitution of BUdR for thymine in “old” DNA strands

Metaphases collected from cultures grown for three cell cycles in 5-bromodeoxyuridine (BUdR) and then for one or two further cell cycles without BUdR show persistence of differentially FPG-stained chromatids. The cell cycle length is not altered by the presence of BUdR. After removal of BUdR, the cells synthesize DNA and incorporate mainly thymine, as demonstrated by density gradient analysis of DNA. Our observations suggest that chromatids with T-B DNA stain lightly after removal of BUdR, in contrast with their dark staining when cultures are maintained in BUdR. Thus, in any experimental condition, there is a correspondence between the nature (T-DNA or B-DNA) of the “old” DNA strands and the FPG-staining (dark or light) of the chromatids.     

Speciation and the “shifting balance” in a continuous population

Shifts between adaptive peaks, caused by sampling drift, are involved in both speciation and adaptation via Wright's “shifting balance.” We use techniques from statistical mechanics to calculate the rate of such transitions for a population in a single panmictic deme and for a population which is continuously distributed over one- and two-dimensional regions. This calculation applies in the limit where transitions are rare. Our results indicate that stochastic divergence is feasible despite free gene flow, provided that neighbourhood size is low enough. In two dimensions, the rate of transition depends primarily on neighbourhood size N and only weakly on selection pressure (≈s^k exp(− cN)), where k is a number determined by the local population structure, in contrast with the exponential dependence on selection pressure in one dimension (≈exp(− cN √s)) or in a single deme (≈exp(− cNs)). Our calculations agree with simulations of a single deme and a one-dimensional population.     

Protein synthesis during fetal development of mouse epidermis : I. The appearance of “histidine-rich protein”

The synthesis of specific proteins at different stages in the development of mouse epidermis was investigated. The epidermis from mice of an age range from 16 days of fetal life to 7 weeks postpartum was prepared by maceration in acetic acid, and the total proteins were separated by SDS-polyacrylamide gel electrophoresis. The appearance of particular proteins at different developmental stages was correlated with the morphology of the epidermis at the same stage. Several qualitative and quantitative changes in the protein patterns were observed during development, the significance of which is discussed. A protein of molecular weight approximately 27,000 was the major component of a group of closely related proteins which appeared simultaneously with the production of mature keratohyalin granula in 18-day fetal mouse epidermis. Isolation and characterization of this protein showed it to be a “histidine-rich protein.” Its concentration in the epidermis decreased as the number of keratohyalin granula diminished with increasing age. The protein could be localized exclusively in the keratohyalin granula by a fluorescence method involving staining with dansyl chloride. This method was also used to detect “histidine-rich protein” on polyacrylamide gels.     

Turbulence, watermass stratification and harmful algal blooms: an alternative view and frontal zones as “pelagic seed banks”

Watermass stratification has been considered the essential physical condition that dinoflagellates require to bloom because of their relative inability, unlike diatoms, to tolerate the elevated shear-stress associated with water-column mixing, turbulence and high velocity, coastal currents. The swimming speeds of 71 flagellate taxa, with a focus on dinoflagellates, are compared to the turbulence fields and vertical velocities that develop during representative wind conditions, upwelling and at frontal zones. The results suggest that the classical stratification–dinoflagellate bloom paradigm needs revision. Tolerance of turbulence, growth within well-mixed watermasses and survival and dispersal while entrained within current systems are well developed capacities among dinoflagellates. Their secretion of mucous, often copious during blooms, is suggested to be an environmental engineering strategy to dampen turbulence. Biophysical tolerance of turbulence by dinoflagellates is often accompanied by high swimming speeds. Motility speeds of many species exceed in situ vertical current velocities; this also allows diel migrational patterns and other motility-based behavior to persist. Species belonging to “mixing-drift” life-form assemblages can increase their swimming speeds through chain formation, which helps to compensate for the increased turbulence and vertical water-column velocities of their habitats. The ability of dinoflagellate species to tolerate the vertical velocities of offshore, frontal zones, where abundant populations often develop, suggests that fronts may serve as “pelagic seed banks”, occurring as pelagic analogues of nearshore seed beds, from which seed stock is dispersed. The different ecologies associated with the hypothesized, “pelagic seed banks” of vegetative cells and the “seed beds” of resting stage cells deposited onto sediments are discussed. There is a contradiction in the stratification–HAB paradigm: the quiescent conditions of a stratified watermass, with its characteristic nutrient-poor conditions are expected to promote stasis of the population, rather than growth and blooms. The analyses suggest that dinoflagellate blooms do not preponderate in stratified watermasses because the bloom species are biophysically intolerant of the higher velocities and turbulence of more mixed watermasses. The watermass stratification that often accompanies flagellate blooms is probably a secondary, parallel event and less essential than some other factor(s) in triggering the observed bloom.     

Remotely-sensed indicators for monitoring the general condition of “natural habitat” in watersheds: an application for Delaware’s Nanticoke River watershed

Over the past two decades there has been increasing interest in developing indicators to monitor environmental change. Remote sensing techniques have been primarily used to generate information on land use/land cover changes. The US Fish and Wildlife Service has used this technology to monitor wetland trends and recently developed a set of remotely-sensed indicators to characterize and assess trends in the integrity of natural habitat in watersheds. The indices largely focus on the extent of “natural” cover throughout a given watershed, with an emphasis on locations important to fish, wildlife, and water quality. Six indices address natural habitat extent and four deal with human-caused disturbance. A composite index of natural habitat integrity combining the habitat extent and habitat disturbance indices may be formulated to provide an overall numeric value for a watershed or subbasin. These indices facilitate comparison between watersheds (and subbasins) and assesssment of trends useful for environmental monitoring. This paper describes the indices and presents an example of their application for characterizing and assessing conditions of subbasins within Delaware’s Nanticoke River watershed.