Conservative trees have universal segment measure distributions

It is shown that “conservative” trees, which posses some measure that is conserved across branchpoints, generate a distribution of the measure over the segments that is approximately hyperbolic. When the trees become large, the shape of the distribution becomes independent of drastic changes in the asymmetry of the branching, in the measure distribution of the root segments, or in the valency of the branchpoints. In contrast to the invariant shape, the amplitude of the distribution does depend on the above parameters, but it can be computed numerically or, in many important cases, analytically. These results can be used to compute the distribution of related (but nonconserved) quantities of the trees, to solve the scaling problem of large trees, and to gain insight into the relations between local and global consequences of dendritic growth.     

Macroscopic and microscopic variation in recovered magnesium phosphate materials: Implications for phosphorus removal processes and product re-use

Phosphorus (P) recovery and re-use will become increasingly important for water quality protection and sustainable nutrient cycling as environmental regulations become stricter and global P reserves decline. The objective of this study was to examine and characterize several magnesium phosphates recovered from actual wastewater under field conditions. Three types of particles were examined including crystalline magnesium ammonium phosphate hexahydrate (struvite) recovered from dairy wastewater, crystalline magnesium ammonium phosphate hydrate (dittmarite) recovered from a food processing facility, and a heterogeneous product also recovered from dairy wastewater. The particles were analyzed using “wet” chemical techniques, powder X-ray diffraction (XRD), and scanning electron microscopy in conjunction with energy dispersive X-ray spectroscopy (SEM–EDS). The struvite crystals had regular and consistent shape, size, and structure, and SEM–EDS analysis clearly showed the struvite crystals as a surface precipitate on calcium phosphate seed material. In contrast, the dittmarite crystals showed no evidence of seed material, and were not regular in size or shape. The XRD analysis identified no crystalline magnesium phosphates in the heterogeneous product and indicated the presence of sand particles. However, magnesium phosphate precipitates on calcium phosphate seed material were observed in this product under SEM–EDS examination. These substantial variations in the macroscopic and microscopic characteristics of magnesium phosphates recovered under field conditions could affect their potential for beneficial re-use and underscore the need to develop recovery processes that result in a uniform, consistent product.     

Perinatal adaptation in mammals: the impact of metabolic rate

Mammalian birth is accompanied by profound changes in metabolic rate that can be described in terms of body size relationship (Kleiber's rule). Whereas the fetus, probably as an adaptation to the low intrauterine pO₂, exhibits an “inappropriately” low, adult-like specific metabolic rate, the term neonate undergoes a rapid metabolic increase up to the level to be expected from body size. A similar, albeit slowed, “switching-on” of metabolic size allometry is found in human preterm neonates whereas animals that are normally born in a very immature state are able to retard or even suppress the postnatal metabolic increase in favor of weight gain and O₂ supply. Moreover, small immature mammalian neonates exhibit a temporary oxyconforming behavior which enhances their hypoxia tolerance, yet is lost to the extent by which the size-adjusted metabolic rate is “locked” by increasing mitochondrial density. Beyond the perinatal period, there are no other deviations from metabolic size allometry among mammals except in hibernation where the temporary “switching-off” of Kleiber's rule is accompanied by a deep reduction in tissue pO₂. This gives support to the hypothesis that the postnatal metabolic increase represents an “escape from oxygen” similar to the evolutionary roots of mitochondrial respiration, and that the overall increase in specific metabolic rate with decreasing size might contribute to prevent tissues from O₂ toxicity.     

Visual shape recognition with contour propagation

A neural architecture is presented that encodes the visual space inside and outside of a shape. The contours of a shape are propagated across an excitable neuronal map and fed through a set of orientation columns, thus creating a pattern which can be viewed as a vector field. This vector field is then burned as synaptic, directional connections into a propagation map, which will serve as a “shape map”. The shape map identifies its own, preferred input when it is translated, deformed, scaled and fragmented, and discriminates other shapes very distinctively. Encoding visual space is much more efficient for shape recognition than determining contour geometry only.     

The relationship between reproductive success and demographic structure in remnant populations of Primula veris

Plants often suffer reductions in fecundity due to fragmentation, degradation and destruction of populations and their sites. Whether this decrease in seed production has population-level consequences is generally unknown. Here, we aimed to determine the current status of remnant populations in the perennial herb Primula veris in Belgium. Furthermore, we investigated the effects of reduced population size and morph bias on reproductive success and explored if changes in demographic structure could be associated with population fecundity. We studied 69 populations that differed in population size from three to nearly 1500 flowering plants. Three different population types could be distinguished: (a) “dynamic” populations, characterized by high densities of 1 year old juveniles, (b) “normal” populations with adult age-stages prevailing, but still a considerable number of juveniles, and (c) “regressive” populations, in which only flowering adults dominate and rejuvenation hardly occurs. The three population types differed with respect to population size and morph frequency. Dynamic populations were significantly larger and showed a weaker morph bias compared to the intermediate normal and the small regressive populations. Reproductive success, studied the previous year in 26 populations, decreased significantly with decreasing population size and was significantly associated with the demographic structure of the populations. Coefficients of variation for the proportion of flowers setting fruit, the number of seeds per fruit and the total number of seeds per plant decreased significantly with increasing population size. Hence, the observed variability in seed set may be one of the causal factors affecting the observed types of population demographic structure.     

Crystalline inclusions in hepatocytes and associated interhepatocytic macrophages from female Ohrid trout (Salmo letnica Kar.)

When characterizing the liver ultrastructure in Ohrid trout, we noticed that cells often displayed unusual cytoplasmic crystalline inclusions. Their morphology varied much, concerning the size, shape and electron density, showing aspects never reported in fish liver. In hepatocytes, the inclusions existed in close topographical relationship with dense bodies (often within them). Such “crystals” inclusions also existed in macrophages and in biliary passages lumina. Data revealed seasonal/breeding-related changes of the dense bodies and crystalline inclusions within hepatocytes; decreasing from the earliest to the more advanced ovary maturation stages. Additionally, based on the negative correlations between the amounts of dense bodies and of “crystals” and the ovary somatic ratio, we suggested there might be connections between the sex steroids status and the inclusions formation. A positive correlation between the quantities of “crystals” and of dense bodies further suggested that the inclusions might derive from normal processes, e.g., the females’ cyclic liver changes, that involves dense bodies’ turnover. However, a toxicological aetiology cannot be excluded. Additionally, multiple mechanisms can contribute to the “crystals” genesis. Facing literature reports and because the inclusions content seemed washed out during tissue processing, they are likely lipid in nature, but their exact composition and genesis require further analyses.     

Morphometric parameters of neurons in reticular nuclei of the brain stem in kittens

Three types of Golgi-stained neurons were discovered in brain stem reticular nuclei of 30-day-old kittens: sparsely branching reticular neurons, those with densely branching dendritic trees, and giant multipolar neurons (Leontovich's classification). Adopting computerized morphometric techniques enabled 23 different parameters to be measured in cells of these types. The measurements taken from the neuronal groups investigated revealed statistically significant differences between them for most parameters. It was concluded from this that each of the neuronal types distinguished has its own morphological identity (or stability). Characteristics of structural differences and properties of differing cell types in reticular nuclei are discussed in relation to their functional properties.Institute of Higher Nervous Activity and Neurophysiology, Academy of Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 23, No. 4, pp. 399–409, July–August, 1991.     

Rapid monitoring of cell size, vitality and lipid droplet development in the oleaginous yeast Waltomyces lipofer

The aim of this work was the development of rapid methods suitable for monitoring the growth of the oleaginous yeast Waltomyces lipofer by means of cell size, vitality and the development of internal lipid droplets throughout different growth phases. Oleaginous yeasts are of interest for the industrial production of lipids and therefore precise monitoring of growth characteristics is needed.This paper provides information about both the method development as well as about examples for their use in monitoring applications. Cell size and shape were determined using FPIA (Flow Particle Image Analysis). Vitality and internal lipid droplets were measured using two independent staining methods for Flow Cytometry. Double staining with cFDA & PI was used for the distinction between “vital”, “sublethal” and “dead” subpopulations, whereas Nile Red allowed the monitoring of lipid accumulation. In this approach the method for vitality measurement was optimized focussing on the staining buffer. An addition of 25 mM citric acid and pH 4.8 revealed to be optimal. The cells in the growth experiment showed a constantly high vitality, which was always above 90%, but slowly decreasing over time. In the course of lipid droplet development it could be seen that the cell size and the Nile Red fluorescence intensity increased. It was demonstrated that the tested method combination provides a powerful tool for rapid fermentation monitoring of the oleaginous yeast W. lipofer, which allows gaining information about the desired growth characteristics in less than 45 min. Further applications for the two methods will be discussed in this article.     

Differentiation of human adipose-derived adult stem cells into neuronal tissue: Does it work?

Adipose tissue contains many cells and proteins that are of value not only for their potential therapeutic applications, but also for the low cost of their harvest and delivery. Mesenchymal stem cells (MSC) were originally isolated from the bone marrow, although similar populations have been isolated from adipose and other tissues. At one time, neural tissues were not regarded as regenerative populations of cells. Therefore, the identification of cell populations capable of neuronal differentiation has generated immense interest. Adipose tissue may represent an alternative source of cells that are capable of neuronal differentiation, potentially enhancing its use in the treatment of neurological disease. The aim of this review is to cover the current state of knowledge of the differentiation potential of human adipose-derived stem (ADAS) cells, specifically their ability to give rise to neuronal cells in vitro. This review presents and discusses different protocols used for inducing human ADAS cells to differentiate in vitro, and the neuronal markers utilized in each system.     

Protein tyrosine phosphatase PTPRT as a regulator of synaptic formation and neuronal development

PTPRT/RPTPρ is the most recently isolated member of the type IIB receptor-type protein tyrosine phosphatase family and its expression is restricted to the nervous system. PTPRT plays a critical role in regulation of synaptic formation and neuronal development. When PTPRT was overexpressed in hippocampal neurons, synaptic formation and dendritic arborization were induced. On the other hand, knockdown of PTPRT decreased neuronal transmission and attenuated neuronal development. PTPRT strengthened neuronal synapses by forming homophilic trans dimers with each other and heterophilic cis complexes with neuronal adhesion molecules. Fyn tyrosine kinase regulated PTPRT activity through phosphorylation of tyrosine 912 within the membrane-proximal catalytic domain of PTPRT. Phosphorylation induced homophilic cis dimerization of PTPRT and resulted in the inhibition of phosphatase activity. BCR-Rac1 GAP and Syntaxin-binding protein were found as new endogenous substrates of PTPRT in rat brain. PTPRT induced polymerization of actin cytoskeleton that determined the morphologies of dendrites and spines by inhibiting BCR-Rac1 GAP activity. Additionally, PTPRT appeared to regulate neurotransmitter release through reinforcement of interactions between Syntaxin-binding protein and Syntaxin, a SNARE protein. In conclusion, PTPRT regulates synaptic function and neuronal development through interactions with neuronal adhesion molecules and the dephosphorylation of synaptic molecules. [BMB Reports 2015; 48(5): 249-255]     

Quantitative characteristic of the catalytic properties and microstructure of cross-linked enzyme aggregates of penicillin acylase

The microstructure and the catalytic properties of cross-linked enzyme aggregates (CLEA) of penicillin acylase (PA) obtained under different conditions were investigated. The period of time left between the enzyme precipitation and the cross-linking step was found to influence the structural organization of the resulting enzyme preparation. Confocal fluorescent microscopy of the so-called “fresh” and “mature” CLEAs PA allowed to estimate the “characteristic” diameter of CLEA PA particles, which appeared to be about 1.6 μm, and revealed that the “mature” type was composed of relatively big particles as compared to the “fresh” type. Complementary kinetic studies showed that the “mature” CLEA PA were more effective in both hydrolytic and synthetic reactions. It was suggested that the aggregate size might regulate the extent of covalent modification of PA and thereby influence the catalytic properties of CLEA.     

Biosynthesis, mode of action and functional significance of neurosteroids in the developing Purkinje cell

New findings over the past decade have shown that the brain has the capability of forming steroids de novo from cholesterol, the so-called “neurosteroids”. To understand neurosteroid action in the brain, data on the regio- and temporal-specific synthesis of neurosteroids are needed. Recently, we have demonstrated that the Purkinje cell, a cerebellar neuron, is a major site for neurosteroid formation in a variety of vertebrates. This is the first demonstration of de novo neuronal neurosteroidogenesis in the brain. Since this discovery, organizing actions of neurosteroids are becoming clear by the studies on mammals using the Purkinje cell as an excellent cellular model. In mammals, the Purkinje cell actively synthesizes progesterone de novo from cholesterol during neonatal life, when cerebellar neuronal circuit formation occurs. The Purkinje cell may also produces estradiol in the neonate. Interestingly, both progesterone and estradiol promote dendritic growth, spinogenesis and synaptogenesis via each cognate nuclear receptor in the developing Purkinje cell. Such organizing actions may contribute to the formation of cerebellar neuronal circuit during neonatal life. This paper summarizes the advances made in our understanding of the biosynthesis, mode of action and functional significance of neurosteroids in the developing Purkinje cell.     

Interspersed repeats are found predominantly in the "old" alpha satellite families

The biased distribution of dispersed repeat insertions in various types of primate specific α satellites (AS) is being discussed in the literature in relation to the modes of AS evolution and their possible roles in maintenance and disruption of functional centromeres. However, such a bias has not been properly documented on a genome-wide scale so far. In this work, using a representative sample of about 100 insertions we show that the “old” AS contains at least 10 times more dispersed repeats than the “new” one. In the new arrays insertions accumulate mostly in poorly homogenized areas, presumably in the edges, and in the old AS, throughout the whole array length. Dating of L1 insertions in the old AS revealed that their massive accumulation started at or after the time when the new AS emerged and expanded in the genome and the centromere function had shifted to the new AS arrays.     

Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment

Background

The increasing abundance of neuromorphological data provides both the opportunity and the challenge to compare massive numbers of neurons from a wide diversity of sources efficiently and effectively. We implemented a modified global alignment algorithm representing axonal and dendritic bifurcations as strings of characters. Sequence alignment quantifies neuronal similarity by identifying branch-level correspondences between trees.

Results

The space generated from pairwise similarities is capable of classifying neuronal arbor types as well as, or better than, traditional topological metrics. Unsupervised cluster analysis produces groups that significantly correspond with known cell classes for axons, dendrites, and pyramidal apical dendrites. Furthermore, the distinguishing consensus topology generated by multiple sequence alignment of a group of neurons reveals their shared branching blueprint. Interestingly, the axons of dendritic-targeting interneurons in the rodent cortex associates with pyramidal axons but apart from the (more topologically symmetric) axons of perisomatic-targeting interneurons.

Conclusions

Global pairwise and multiple sequence alignment of neurite topologies enables detailed comparison of neurites and identification of conserved topological features in alignment-defined clusters. The methods presented also provide a framework for incorporation of additional branch-level morphological features. Moreover, comparison of multiple alignment with motif analysis shows that the two techniques provide complementary information respectively revealing global and local features.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0605-1) contains supplementary material, which is available to authorized users.     

Concept of functional imaging of memory decline in Alzheimer’s disease

Functional imaging methods such as Positron Emission Tomography (PET) and functional Magnetic Resonance Imaging (fMRI) have contributed inestimably to the understanding of physiological cognitive processes in the brain in the recent decades. These techniques for the first time allowed the in vivo assessment of different features of brain function in the living human subject. It was therefore obvious to apply these methods to evaluate pathomechanisms of cognitive dysfunction in disorders such as Alzheimer’s disease (AD) as well. One of the most dominant symptoms of AD is the impairment of memory. In this context, the term “memory” represents a simplification and summarizes a set of complex cognitive functions associated with encoding and retrieval of different types of information. A number of imaging studies assessed the functional changes of neuronal activity in the brain at rest and also during performance of cognitive work, with regard to specific characteristics of memory decline in AD. In the current article, basic principles of common functional imaging procedures will be explained and it will be discussed how they can be reasonably applied for the assessment of memory decline in AD. Furthermore, it will be illustrated how these imaging procedures have been employed to improve early and specific diagnosis of the disease, to understand specific pathomechanisms of memory dysfunction and associated compensatory mechanisms, and to draw reverse conclusions on physiological function of memory.     

The Neuroblast Assay: An Assay for the Generation and Enrichment of Neuronal Progenitor Cells from Differentiating Neural Stem Cell Progeny Using Flow Cytometry

Neural stem cells (NSCs) can be isolated and expanded in large-scale, using the neurosphere assay and differentiated into the three major cell types of the central nervous system (CNS); namely, astrocytes, oligodendrocytes and neurons. These characteristics make neural stem and progenitor cells an invaluable renewable source of cells for in vitro studies such as drug screening, neurotoxicology and electrophysiology and also for cell replacement therapy in many neurological diseases. In practice, however, heterogeneity of NSC progeny, low production of neurons and oligodendrocytes, and predominance of astrocytes following differentiation limit their clinical applications. Here, we describe a novel methodology for the generation and subsequent purification of immature neurons from murine NSC progeny using fluorescence activated cell sorting (FACS) technology. Using this methodology, a highly enriched neuronal progenitor cell population can be achieved without any noticeable astrocyte and bona fide NSC contamination. The procedure includes differentiation of NSC progeny isolated and expanded from E14 mouse ganglionic eminences using the neurosphere assay, followed by isolation and enrichment of immature neuronal cells based on their physical (size and internal complexity) and fluorescent properties using flow cytometry technology. Overall, it takes 5-7 days to generate neurospheres and 6-8 days to differentiate NSC progeny and isolate highly purified immature neuronal cells.     

The fate of persisting thoracic neurons during metamorphosis of the meal beetle Tenebrio molitor (Insecta: Coleoptera)

Summary A set of motor neurons and interneurons in the thoracic nervous system of the meal beetle Tenebrio molitor L. is described that persist during metamorphosis. The motor neurons under discussion innervate the thoracic ventral longitudinal muscles and were identified by retrograde transport of intramuscularly injected horseradish peroxidase. Persisting motor neurons exhibit a complex repetitive pattern that changes only slightly during development. Additionally, the characterization of serotonin-immunoreactive neurons defines a complex set of interneurons that also persist throughout development. The fate of these identified neurons is outlined in detail with special reference to variations in their dendritic arborizations. All motor and interneurons are affected by a similar change in their shape during development. The larval neurons lack the contralateral arborization that is found in the adult beetle and is already distinguishable in the prepupa. Essentially only quantitative changes of the neuronal shape were observed during the pupal instar. No pupa-specific degeneration of certain axo-dendritic structures of these neurons was found. Removal of descending interneurons by sectioning the promesothoracic connectives causes specific degeneration of the dendritic tree of an identified serotonin-immunoreactive interneuron.     

Characterization of synchronized bursts in cultured hippocampal neuronal networks with learning training on microelectrode arrays

Spontaneous synchronized bursts seem to play a key role in brain functions such as learning and memory. Still controversial is the characterization of spontaneous synchronized bursts in neuronal networks after learning training, whether depression or promotion. By taking advantages of the main features of the microelectrode array (MEA) technology (i.e. multisite recordings, stable and long-term coupling with the biological preparation), we analyzed changes of spontaneous synchronized bursts in cultured hippocampal neuronal networks after learning training. And for this purpose, a learning model at networking level on MEA system was constructed, and analysis of spontaneous synchronized burst activity modulation was presented. Preliminary results show that, the number of burst was increased by 154%, burst duration was increased by 35%, and the number of spikes per burst was increased by 124%, while interburst interval decreased by 44% with learning. In particular, correlation and synchrony of neuronal activities in networks were enhanced by 51% and 36%, respectively, with learning. In contrast, dynamic properties of neuronal networks were not changed much when the network was under “non-learning” condition. These results indicate that firing, association and synchrony of spontaneous bursts in neuronal networks were promoted by learning. Furthermore, from these observations, we are encouraged to think of a more engineered system based on in vitro hippocampal neurons, as a novel sensitive system for electrophysiological evaluations.     

On the concept of the effective population size

The concept of the effective population size is discussed. It is shown that the “eigenvalue” and the “inbreeding” effective population sizes are in principle different, even though they have been sometimes identified in the literature. On the other hand the “eigenvalue” and “variance” effective sizes are usually both close when the latter exists. Since, however, there are many models for which a variance effective size cannot in principle exist, it seems useful to introduce the eigenvalue effective size and to examine some of its properties.