Advanced methods for bioreactor characterization.

Bioreactors are characterized by the transport capacities they provide to optimally supply the microorganisms during production process. The transport is performed by flows induced in their cultivation media. In order to understand the extremely complex mixing, mass and heat transfer phenomena encountered, and to perceive their influences on bioreactor performance, sophisticated measuring techniques are required. This review compiles the developments currently in progress to surmount today's shortage of reliable measuring techniques. Measuring techniques are distinguished which can be used on different scales and their application spectra are illustrated by recently obtained results. Several new measuring techniques, which can be employed to resolve the flow structures, are discussed in detail. Only those techniques are considered which can be used to advantage during real cultivations in industrial-scale reactors.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Diagnosis of Dermatophytosis

Dermatophytoses are infections of the skin, hair or nails caused by dermatophytes. Dermatophytes can induce typical diagnostic clinical lesions (tinea), but can also mimic other dermatoses. Therefore, physicians need to be familiar with the whole spectrum of tinea and must constantly be mindful of possible dermatophytosis. An examination with Wood’s light can be helpful. In superficial lesions, the demonstration of dermatophytes may be achieved by dermatoscopy or laser scanning. An essential step of the following diagnostic procedure is the skilful collection of samples for the proof of fungi. Microscopy of KOH mounts or equivalent preparations produced from infected material and histology are approved methods. The necessary identification of dermatophytes on species level can finally be accomplished by conventional methods based on cultures or by new techniques based on molecular differentiation or MALDI-TOF analysis. These modern methods are clearly on the increase and can considerably improve and accelerate dermatophyte identification.     

The ecology of granite outcrops at Wilson's Promontory,Victoria

Rock outcrops on spurs and summits on Wilson's Promontory tend to be more prevalent on hot dry slopes than cool moist ones. In this comparatively moist climate, the rock outcrop vegetation can be grouped into high altitude, low altitude and coastal types. The surrounding rock-heath is characterized below 400–500 m by Kunzea ambigua and above this altitude by Callistemon pallidus. Moss aprons of Campylopus bicolor on rock faces are often held in place by roots of surrounding shrubs on slopes up to 20°. Bryophyte and lichen communities vary with altitude, and annuals and geophytes are common. Fire may result in retrogression if forests and shrub zones are destroyed and humic top soil burnt or eroded away. Fossil root-grooves occur in granite on the summit of Mt Latrobe and are the legacy of a cloud forest of Nothofagus cunninghamii. The rock-heath species are more drought resistant than the‘climax’tree species and may develop very low water potentials. The rate of succession may be correlated with the highly variable rate of decay of each individual block of granite. The soils of the early successional stages are veneers of humic sands enriched with hill-wash, whilst the soils of the forest stages vary from duplex podzols to gradational podzolic soils of much greater moisture storage. Woody plant establishment is mostly initiated along rock joints: the rock surfaces and boulders so by-passed are colonized by more mesic species. Many zonations appear to be static since advances are cancelled by retreats. The rate of succession on bare granite is controlled by local climate, altitude, slope, fire and macro-and micro-jointing patterns. In general, the early stages bear strong similarities over a relatively wide range of climate. The so-called climaxes which have developed represent a continuum in response to the complex environments found on Wilson's Promontory.     

蓝细菌基因组拷贝数的研究进展与展望

蓝细菌是一类古老的光合原核微生物。就基因组拷贝数(倍性)而言,蓝细菌是原核生物中基因组低、中、高拷贝共存的典型类群之一,而基因组多拷贝特性是制约蓝细菌高效遗传改造的瓶颈。已有研究表明,蓝细菌的基因组拷贝数表现出生长周期的依赖性并受多种遗传、环境因子的影响。文中综述了蓝细菌基因组拷贝数的国内外最新研究进展、分析方法及影响因素,并讨论了蓝细菌基因组多拷贝研究的环境生态和生物技术意义。最后,对未来蓝细菌基因组拷贝数相关的研究方向作出展望。     

Studies of collagen fold formation in aqueous solutions of alpha-gelatin III

Optical rotation, viscosity, and density studies are reported on solutions of α-gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.     

Of crazy-ants and Curetinae: are Curetis butterflies tended by ants?

The larvae of the lycaenid subfamily Curetinae have never been reported to be associated with ants. Observations on Curetis regula Evans from Brunei are presented which show that this species may be tended by ants both as larvae and adults. The observations are discussed in relation to a recent review on lycaenid/ant associations, u is suggested that the Curetinae will be found to be associated with ants when more species have been reared, on evidence of the larval tentacle organs and apparent 'pore cupolas', both of which are ant adaptations. More studies are needed on Curetis biology and larval morphology to resolve the relationships of this enigmatic genus within the Lycaenidae.     

Melatonin mediates seasonal adjustments in immune function.

In addition to seasonal changes in reproductive function, seasonal changes in immune function are mediated by the pineal hormone, melatonin. Melatonin affects immune function both indirectly, acting through other hormones, and directly by acting on components of the immune system. Melatonin also affects tumorigenesis and tumor development. We hypothesize that many of the indirect effects of melatonin on immune function are mediated through glucocorticoids, and appear to be part of an integrated series of adaptations to manage energy. Direct effects of melatonin on immune function appear to be mediated by melatonin receptors on lymphatic tissue or on immune cells in circulation. Winter is energetically demanding and stressful; thermoregulatory demands typically increase when food availability decreases. Individuals would enjoy a survival advantage if seasonally recurring stressors could be anticipated and countered by bolstering immune function. To summarize, melatonin may be part of an integrative system to coordinate reproductive, immunologic and other physiological processes to cope successfully with energetic stressors during winter.     

Physicians in health care management: 2. Managing performance: who,what, how and when?

Physicians are becoming more involved in performance management as hospitals restructure to increase effectiveness. Although physicians are not hospital employees, they are subject to performance appraisals because the hospitals are accountable to patients and the community for the quality of hospital services. The performance of a health care professional may be appraised by the appropriate departmental manager, by other professionals in a team or program or by peers, based on prior agreement on expectations. Appraisal approaches vary. They include behavioural approaches such as rating scales, peer rating, ranking or nomination and outcome approaches such as management by objectives and goal setting. Professionals should give and receive timely feedback on a flexible schedule. Feedback can be provided one-on-one, by a group assessing quality of care or through an anonymous survey.     

The interpretation of oligonucleotide maps. A theoretical study of nucleic acid digests with special reference to repeated diverged sequences

Oligonucleotide mixtures produced by the digestion of RNA by specific nucleases can be defined in terms of isostichs (sets of common chain length), compositional isomers, and sequence isomers. Equations are derived to express the distribution of radioactivity on the isostich length, the distribution of compositional isomers on the isostich length, and the distribution of compositional isomers on the proportion of total radioactivity (“intensity”). It is shown how the properties of a “fingerprint” may be calculated from first principles, and conversely how the complexity of a sequence may be estimated from its fingerprint. The equations are tested by means of computer simulations of RNA digestions and their range of applicability is determined. The three distributions are used to analyze the digests of repetitious sequences. It is shown how the parameters of a diverged sequence family can, in a favorable case, be deduced from its fingerprint.     

Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side.     

Population genetic models of male and mutual mate choice

Examples of male mate choice are becoming increasingly common, even in polygynous species. We create a series of population genetic models to examine the evolutionary equilibria and dynamics resulting from male mate choice during polygyny, alone and in the context of mutual mate choice by both sexes. We find that unless males with a preference are able to increase their overall courtship output, male preference will be lost. This loss can be counteracted if males choose females not based on arbitrary traits, but based on a trait that indicates high fertility or viability. We also conclude that if male and female preferences and traits are all controlled by different loci, the male and female mate choice systems are decoupled; the presence of a male preference then has no influence on the equilibria or dynamics of female mate choice. If male and female traits are coupled by pleiotropy, it becomes possible for a male preference to be maintained, regardless of whether preferences between the sexes are pleiotropic or controlled by separate loci.     

Cell size and mutual cell adhesion. II. Evidence for a relation between cell size, long-range electrostatic repulsion and intercellular adhesiveness during density-regulated growth in suspension.

The strength of the long-range electrostatic repulsion forces on HeLa cells is measured by agglutinative titration using low molecular weight polylysine (M.W. 11,000). Repulsion forces, found to be present on the smaller HeLa cells from density-inhibited suspension cultures, are weakened by incubation of the cells in hypotonic NaCl solutions. Repulsion forces, found to be absent on the larger cells from fast growing cultures, can be induced on these cells by incubation in hypertonic NaCl solutions. Both effects of anisotonicity are reversible, and disappear on restoration of the medium to normal tonicity. Induction of repulsion forces on fast growing cells is prevented by previous treatment of the cells with neuraminidase. Neuraminidase also abolishes repulsion on density-inhibited cells. It is proposed that alterations of the cell size, produced by anisotonicity or occurring during growth in isotonic suspension medium, affect mutual cell adhesiveness by modifying the strength of the repulsion forces generated by cell surface sialic acids.     

A statistical approach for array CGH data analysis

Background  

Microarray-CGH experiments are used to detect and map chromosomal imbalances, by hybridizing targets of genomic DNA from a test and a reference sample to sequences immobilized on a slide. These probes are genomic DNA sequences (BACs) that are mapped on the genome. The signal has a spatial coherence that can be handled by specific statistical tools. Segmentation methods seem to be a natural framework for this purpose. A CGH profile can be viewed as a succession of segments that represent homogeneous regions in the genome whose BACs share the same relative copy number on average. We model a CGH profile by a random Gaussian process whose distribution parameters are affected by abrupt changes at unknown coordinates. Two major problems arise : to determine which parameters are affected by the abrupt changes (the mean and the variance, or the mean only), and the selection of the number of segments in the profile.     

Life on Jupiter?

The possibilities of life on Jupiter are discussed from the point view of life as we know it. That is, we assume that any life on Jupiter would not involve new principles foreign to us. Proteins would be a constituent as would fats and the other building blocks of living organisms on Earth. This leads us to a set of limiting parameters, such as pressure. Studies in the laboratory have shown that proteins and other essential molecules are denatured by pressures of 4000 atm and higher. Thus, we must not expect life in the great depths of the Jovian atmosphere. It could exist only at depths of several hundred kilometers in the atmosphere. Since no solid surface could possibly exist at such altitudes, any organisms present must be small enough to be buoyed up by the turbulent atmospheric currents or must fly or both. Such possibilities, however, seem to be real. The necessary nutrients to preserve life and foster growth could be furnished by the Miller-Urey type reactions of lonizing radiation on the reducing atmosphere undoubtedly present. There can, of course, be no possibility of oxygen on Jupiter, and so the life forms, if they exist, must be anaerobic. Such possibilities are real and have often been cited in connection with the origin of life on Earth.     

The importance of validated ecological indicators for manure regulations in the Netherlands

The termination of the EU milk quota system on April 1, 2015 is leading to an increase in manure production in the Netherlands. Rather than focus on the quality of water and nature, of which at least the water quality has strongly improved during the last decades, discussions appear to center on strengthening proxy measures that are already being used and which are only remotely related to the quality issue. The quality of water and nature is determined for ground- and surface water by first measuring their N and P content and for nature areas the N deposition. When these values are higher than threshold values determined by ecologists, quality is inadequate and measures are needed. When values are lower, quality is adequate. Three basic problems need to be addressed: (i) threshold values are in practice considered to be permanent while they should be dynamic reflecting a learning process when comparing measurements of N and P values on the one hand and a simultaneous ecological characterization on the other. This requires more cooperation between soil scientists, hydrologists and ecologists. Dynamic characterization may well lead to locally different threshold values. (ii) many measurements of water quality are being made but hardly any measurements of N deposition on nature areas. Such measurements are needed to allow judgements as to the effect of agricultural practices on nature quality. (iii) The necessary further improvement in water and nature quality, as far as it is affected by agricultural practices, can only be achieved when farmers are fully committed and engaged. The current top-down regulations with a “command-and-control” character, while effective in the 1990s, cannot serve this purpose in the information age, the more so since farmers are increasingly well educated and ask too many questions that are not being answered. The suggestion is made to change the generic character of the legislation (“one size fits all”) to a system where “tailor made” management systems are designed for individual farms,considering environmental conditions in the area where the farm occurs. Researchers and farmers can work together in a joint-learning mode to develop such designs that can be recognized by certificates with a legal status. In any case, the proportionality principle needs to be considered assuring that the severity of measures taken are in balance with societal effects.     

Signals and Receptors—The Translocation Machinery on the Mitochondrial Surface

Most proteins involved in mitochondrial biogenesis are encoded by the genome of the nucleus.They are synthesized in the cytosol and have to be transported toward and, subsequently,imported into the organelle. This targeting and import process is initiated by the specificmitochondrial targeting signal, which differs pending on the final localization of the protein.The preprotein will be recognized by cytosolic proteins, which function in transport towardthe mitochondria and in maintaining the import competent state of the preprotein. The precursorwill be transferred onto a multicomponent complex on the outer mitochondrial membrane,formed by receptor proteins and the general insertion pore (GIP). Some proteins are directlysorted into the outer membrane whereas the majority will be transported over the outermembrane through the import channel followed by further distribution of those proteins.     

Cyclic adenosine 3',5' monophosphate, calcium and protein phosphorylation in flagellar motility

cAMP and calcium are two important regulators of sperm flagellar motility. cAMP stimulates sperm motility by activating cAMP-dependent protein kinase and catalyzing the phosphorylation of sperm proteins. The stimulation of sperm motility by cAMP appears to be at two different levels. Evidence has been presented to suggest that cAMP-dependent phosphorylations may be required in order for motility to be initiated. In addition, cAMP-dependent phosphorylation appears to modulate specific parameters of motility resulting in higher beat frequency or greater wave amplitude. Calcium, on the other hand, when elevated intracellularly to 10(-6) M or higher, inhibits flagellar motility. The calcium-binding protein, calmodulin, appears to mediate a large number of effects of calcium on motility. Evidence suggests that calcium-calmodulin may be involved at the level of the membrane to pump calcium out of the flagellum. In addition, calcium-calmodulin may be involved in the control of axonemal function by regulating dynein ATPase and myosin light chain kinase activities. The identification of cAMP-dependent protein kinase, calmodulin and myosin light chain kinase in the sperm head suggests that cAMP and calcium-dependent phosphorylations are also involved in the control of the fertilization process, i.e., the acrosome reaction, in a manner similar to that known for the control of stimulus/secretion coupling. Finally, the effects of cAMP on flagellar motility are mediated by protein phosphorylation while the effects of calcium on motility are also in part, mediated by effects on protein phosphorylation.     

Pests controlling pests: does predator control lead to greater European rabbit abundance in Australasia?

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