Morphogenetic Processes: Application to Cambial Growth Dynamics

Both the physiological and the pathological morphogenetic processes that we can meet in embryogenesis, neogenesis and degenerative dysgenesis present common features: they are ruled by three different kinds of mechanisms, one related to cell migration, the second to cell differentiation and the third to cell proliferation. We deal here with an application to the cambial growth which essentially involves the third type of mechanism. Woody plants produce secondary tissue (secondary xylem and phloem) from a meristematic tissue called vascular cambium, responsible for the radial growth of a tree. This paper focuses on the formation of secondary xylem, considered in two dimensions in a cross-section framework. A new discrete modelling approach is used, based on the cellular scale, in order to attain a more accurate understanding of how the elementary microscopic behaviour of each cell takes part in the macroscopic morphogenesis. The mathematical model essentially uses an occurrence method simulating the main features of radial growth with simple geometric rules, such as Thom's division rule (Thom,1972)to account for the cell proliferation. The study applies to concrete instances in which the changes made in the geometrical cellular patterns of the vascular cambium clearly affect the shape of the tree, as in Pinus radiata (D. Don.).     

Role of Glycine in Blood Coagulation Processes

We studied hemocoagulant properties of the amino acid glycinein vitroand after intravenous administration to animals (rats). Addition of 10^–3and 10^–4M glycine to the plasma increases the aggregability of thrombocytesin vitro, while all other test concentrations had virtually no effect on hemostatic parameters of the plasma. Intravenous administration of glycine increased the functional activity of the enzymatic fibrinolytic unit of the anticoagulation system. Dose dependence of this effect has been established. The causes of these changes and possible application of glycine as an agent activating fibrinolysis are discussed.     

Surface Plasmon Dynamics of High-Aspect-Ratio Gold Nanorods

Ultrafast transient absorption studies are reported for high-aspect-ratio gold nanorods that were fabricated by electrochemical deposition in polycarbonate templates. The nanorods are 60 nm in diameter with distribution of lengths of up to 6 μm. The average aspect ratio was ∼50, resulting in a longitudinal surface plasmon resonance (SPR_L) band in the mid-IR, as well as a transverse (SPR_T) band in the visible. The rods were excited at 400 nm and probed at a range of wavelengths from the visible to the mid-IR to interrogate both SPR bands. The dynamics observed, including the electron–phonon coupling time and coherent acoustic breathing mode oscillations, closely resemble those previously reported for gold spherical nanoparticles and smaller-aspect-ratio nanorods. The electron–phonon coupling time was similarly determined to be 3.3 ± 0.2 ps for both of the SPR bands. Also, oscillations with a 32-ps period were observed for probing near the SPR_T band in the visible region due to impulsive coherent excitation of the acoustic breathing mode, which are consistent with the 60-nm diameter of the nanorods determined by scanning electron microscopy. The results demonstrate that the dynamics for long gold nanorods are similar to those for smaller nanoparticles. Gerald M. Sando is a NRL-ASEE Research Associate     

Dynamics of Violence: Processes of Escalation and De-Escalation in Violent Group Conflicts

Dynamics of Violence: Processes of Escalation and De- Escalation in Violent Group Conflicts. Sociologus, Special Publication 1. Georg Elvert. Stephen Feuchtwang. and Dieter Neubert. eds. Berlin: Duncker and Humblot, 1999 290 pp.     

Patterns and Dynamics of Dissolved Organic Carbon (DOC) in Boreal Streams: The Role of Processes,Connectivity, and Scaling

We bring together three decades of research from a boreal catchment to facilitate an improved mechanistic understanding of surface water dissolved organic carbon (DOC) regulation across multiple scales. The Krycklan Catchment Study encompasses 15 monitored nested research catchments, ranging from 3 to 6900 ha in size, as well as a set of monitored transects of forested and wetland soils. We show that in small homogenous catchments, hydrological functioning provides a first order control on the temporal variability of stream water DOC. In larger, more heterogeneous catchments, stream water DOC dynamics are regulated by the combined effect of hydrological mechanisms and the proportion of major landscape elements, such as wetland and forested areas. As a consequence, streams with heterogeneous catchments undergo a temporal switch in the DOC source. In a typical boreal catchment covered by 10-20% wetlands, DOC originates predominantly from wetland sources during low flow conditions. During high flow, the major source of DOC is from forested areas of the catchment. We demonstrate that by connecting knowledge about DOC sources in the landscape with detailed hydrological process understanding, an improved representation of stream water DOC regulation can be provided. The purpose of this study is to serve as a framework for appreciating the role of regulating mechanisms, connectivity and scaling for understanding the pattern and dynamics of surface water DOC across complex landscapes. The results from this study suggest that the sensitivity of stream water DOC in the boreal landscape ultimately depends on changes within individual landscape elements, the proportion and connectivity of these affected landscape elements, and how these changes are propagated downstream.     

Prion Propagation: The Role of Protein Dynamics

The transfer of phenotypes from one individual to another is a fundamental aspect of biology. In addition to traditional nucleic acid-based genetic determinants, unique proteins known as prions can also act as elements of inheritance, infectivity, and disease. Nucleic acids and proteins encode genetic information in distinct ways, either in the sequence of bases in DNA or RNA or in the three dimensional structure of the polypeptide chain. Given these differences in the nature of the genetic repository, the mechanisms underlying the transmission of nucleic acid-based and protein-based phenotypes are necessarily distinct. While the appearance, persistence and transfer of nucleic acid determinants require the synthesis of new polymers, recent studies indicate that prions are propagated through dynamic transitions in the structure of existing protein.Key Words: prion, PrP, [PSI⁺], [URE3], [Het-s], Sup35, Ure2, Het-s, Hsp104     

Prion Propagation: The Role of Protein Dynamics

The transfer of phenotypes from one individual to another is a fundamental aspect of biology. In addition to traditional nucleic acid-based genetic determinants, unique proteins known as prions can also act as elements of inheritance, infectivity, and disease. Nucleic acids and proteins encode genetic information in distinct ways, either in the sequence of bases in DNA or RNA or in the three dimensional structure of the polypeptide chain. Given these differences in the nature of the genetic repository, the mechanisms underlying the transmission of nucleic acid-based and protein-based phenotypes are necessarily distinct. While the appearance, persistence and transfer of nucleic acid determinants require the synthesis of new polymers, recent studies indicate that prions are propagated through dynamic transitions in the structure of existing protein.     

Plasmolipin and Its Role in Cell Processes

Molecular Biology - The mechanisms involved in the origin and development of malignant and neurodegenerative diseases are an important area of modern biomedicine. A crucial task is to identify new...     

Structure and Mechanical Characterization of DNA i-Motif Nanowires by Molecular Dynamics Simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC₅ sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual C⋅C⁺ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression, and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young’s and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.     

Structure and Mechanical Characterization of DNA i-Motif Nanowires by Molecular Dynamics Simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC₅ sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual C⋅C⁺ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression, and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young’s and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.     

Phospholipase D: Its Role in Metabolic Processes and Development of Diseases

Phospholipase D (PLD; EC 3.1.4.4) is one of the key enzymes catalyzing hydrolysis of cell membrane phospholipids. This review considers and summaries current knowledge about six human PLD isoforms, their structure and a role in physiological and pathological processes. Comparative analysis of PLD isoforms structure is presented. The review considers the mechanism of hydrolysis and transphosphatidylation performed by PLD, the role of PLD1 and PLD2 in the pathogenesis of some types of cancer, infectious, thrombotic, and neurodegenerative diseases is analyzed. The prospects of development of PLD isoformselective inhibitors are considered in the context of their clinical use and inclusion into various therapeutic schemes; the latter is especially important in the case of already developed PLD inhibitors. Phosphatidylethanol (PEth) formed in the human body during phospholipid transphosphatidylation catalyzed by PLD is considered as an alcohol abuse biomarker.     

Linking Community and Ecosystem Processes: The Role of Minor Species

The link between species and ecosystem functioning is a central issue in ecology. In natural plant communities, the dominant species determine most of the productivity-related processes but what is the function of minor species? A recent hypothesis suggests that after disturbance, minor species facilitate the recruitment and abundance of dominants during re-colonization, thus indirectly determining ecosystem function. We tested this hypothesis using a long-term dataset of annual plant communities in a semiarid shrubland by comparing plant density and biomass from plots in which all vegetation had been removed; plots from which only the dominant (the annual grass Stipa capensis) had been removed, and control plots. In the absence of vegetation, the dominant failed to re-establish during the following growing season. After being removed the dominant re-established similarly to the controls. An ant exclosure experiment excluded the possibility that this was due to seed predation. In an experiment with individual dispersal units of S. capensis, we demonstrated the mechanism by which minor species can control the dominant’s abundance. Minor species indirectly govern ecosystem processes by providing structures facilitating seed soil penetration and thus recruitment of the dominant.     

Role of the Carrier Frequency in the Territorial Songs of Oscines

Birds cannot emit acoustic signals of very low frequencies. To code a message with such signals they shift them upwards by using a frequency modulation. The new frequency chosen for transmission is the carrier. Its value is adapted to the phonetic and sensory capacities of the bird, as well as to the characteristics of the channel. The code does not give any significance to the carrier alone, but determines its value. Modulation and demodulation must be applied to carriers of the same value. The code also determines the carrier wave shape, i.e. its spectrum. Any alteration of this shape reduces decoding possibilities. To code and decode messages with frequency modulated signals, birds use the same strategies as humans.     

Vanadium in Biosphere and Its Role in Biological Processes

Ultra-trace elements or occasionally beneficial elements (OBE) are the new categories of minerals including vanadium (V). The importance of V is attributed due to its multifaceted biological roles, i.e., glucose and lipid metabolism as an insulin-mimetic, antilipemic and a potent stress alleviating agent in diabetes when vanadium is administered at lower doses. It competes with iron for transferrin (binding site for transportation) and with lactoferrin as it is secreted in milk also. The intracellular enzyme protein tyrosine phosphatase, causing the dephosphorylation at beta subunit of the insulin receptor, is inhibited by vanadium, thus facilitating the uptake of glucose inside the cell but only in the presence of insulin. Vanadium could be useful as a potential immune-stimulating agent and also as an antiinflammatory therapeutic metallodrug targeting various diseases. Physiological state and dose of vanadium compounds hold importance in causing toxicity also. Research has been carried out mostly on laboratory animals but evidence for vanadium importance as a therapeutic agent are available in humans and large animals also. This review examines the potential biochemical and molecular role, possible kinetics and distribution, essentiality, immunity, and toxicity-related study of vanadium in a biological system.     

Imaging Carrier Dynamics and Transport in Hybrid Perovskites with Transient Absorption Microscopy

In this review, the recent progress in using transient absorption microscopy to image charge transport and dynamics in semiconducting hybrid organic–inorganic perovskites is discussed. The basic principles, instrumentation, and resolution of transient absorption microscopy are outlined. With temporal resolution as high as 10 fs, sub‐diffraction‐limit spatial resolution, and excited‐state structural resolution, these experiments have provided crucial details on charge transport mechanisms that have been previously obscured in conventional ultrafast spectroscopy measurements. Morphology‐dependent mapping unveils spatial heterogeneity in carrier recombination and cooling dynamics. By spatially separating the pump and probe beams, carrier transport across grain boundaries has been directly visualized. Further, femtosecond temporal resolution allows for the examination of nonequilibrium transport directly, revealing extraordinarily long‐range hot carrier migration. The application of transient absorption microscopy is not limited to hybrid perovskites but can also be useful for other polycrystalline materials in which morphology plays an important role in carrier transport.     

Dynamics of the Genetic Demographic Structure of the Kursk Oblast Population: Migration Processes

Marriage records from parish books of the second half of the 19th century and marriage records of 1967–1970 and 1993–1995 obtained from registry offices were used to analyze the dynamics of genetically significant parameters of migration and marriage structure with respect to spouses' birthplaces in populations of different hierarchical levels in the Kursk oblast. It was found that, among the persons contracting marriage (both males and females), the proportions of those who were born in the same population and those who were born in any population of the Kursk oblast decreased by about one third and one fifth, respectively, for the 130-year period. In rural and small urban populations, the coefficients of marriage migration in the 19th century were an order of magnitude lower than in the 20th century. The immigration to urban populations was maximum in the late 1960s (m = 0.745 in small towns and m = 0.680 in Kursk), and that to rural populations, in the 1990s (m = 0.344). In both urban and rural populations, the mean distance between the spouses" birthplaces has increased by several times for the period studied. The endogamy level has decreased approximately twofold: from 0.797 to 0.380 in Kursk, from 0.897 to 0.419 in small towns, and from 0.958 to 0.440 in rural districts. The marriage assortativeness with respect to birthplace was maximum in the late 19th century (K = 0.393–0.491) and minimum in the 1960s (K= 0.155–0.246). The increase in genetic diversity of the urban population of the Kursk oblast due to migration has been slowing down since the late 20th century, whereas the outbreeding level is still increasing in rural populations.     

Role of Mitochondrial Dynamics in Neuronal Development: Mechanism for Wolfram Syndrome

Deficiency of the protein Wolfram syndrome 1 (WFS1) is associated with multiple neurological and psychiatric abnormalities similar to those observed in pathologies showing alterations in mitochondrial dynamics. The aim of this study was to examine the hypothesis that WFS1 deficiency affects neuronal function via mitochondrial abnormalities. We show that down-regulation of WFS1 in neurons leads to dramatic changes in mitochondrial dynamics (inhibited mitochondrial fusion, altered mitochondrial trafficking, and augmented mitophagy), delaying neuronal development. WFS1 deficiency induces endoplasmic reticulum (ER) stress, leading to inositol 1,4,5-trisphosphate receptor (IP₃R) dysfunction and disturbed cytosolic Ca²⁺ homeostasis, which, in turn, alters mitochondrial dynamics. Importantly, ER stress, impaired Ca²⁺ homeostasis, altered mitochondrial dynamics, and delayed neuronal development are causatively related events because interventions at all these levels improved the downstream processes. Our data shed light on the mechanisms of neuronal abnormalities in Wolfram syndrome and point out potential therapeutic targets. This work may have broader implications for understanding the role of mitochondrial dynamics in neuropsychiatric diseases.     

Charge Carrier Dynamics of Polymer:Fullerene Blends: From Geminate to Non‐Geminate Recombination

The charge carrier dynamics of a new polymer‐fullerene blend are examined on the femtosecond to the millisecond time scale. The full time range is globally fitted using a chemical reaction rate model that includes all key processes, charge generation, energy transfer, charge separation, and recombination, over the full 12 orders of magnitude in time and a factor of 33 in light intensity. Particular attention is paid to the charge recombination processes and it is found that they are highly material specific. Comparison of the dynamics to those of a previously studied polymer:fullerene blend reveals that while for one blend the recombination dynamics are mainly controlled by geminate recombination, the charge recombination in the presently studied polymer:fullerene blend are entirely controlled by non‐geminate electron‐hole recombination. Carrier density dependence of the non‐geminate recombination rate is analyzed and a correlated disorder model of site energies is proposed to explain the observed dependency.     

Archaeal Population Dynamics during Sequential Reduction Processes in Rice Field Soil

The population dynamics of Archaea after flooding of an Italian rice field soil were studied over 17 days. Anoxically incubated rice field soil slurries exhibited a typical sequence of reduction processes characterized by reduction of nitrate, Fe³⁺, and sulfate prior to the initiation of methane production. Archaeal population dynamics were followed using a dual approach involving molecular sequence retrieval and fingerprinting of small-subunit (SSU) rRNA genes. We retrieved archaeal sequences from four clone libraries (30 each) constructed for different time points (days 0, 1, 8, and 17) after flooding of the soil. The clones could be assigned to known methanogens (i.e., Methanosarcinaceae, Methanosaetaceae, Methanomicrobiaceae, and Methanobacteriaceae) and to novel euryarchaeotal (rice clusters I, II, and III) and crenarchaeotal (rice clusters IV and VI) lineages previously detected in anoxic rice field soil and on rice roots (R. Grosskopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983–4989, 1998). During the initiation of methanogenesis (days 0 to 17), we detected significant changes in the frequency of individual clones, especially of those affiliated with the Methanosaetaceae and Methanobacteriaceae. However, these findings could not be confirmed by terminal restriction fragment length polymorphism (T-RFLP) analysis of SSU rDNA amplicons. Most likely, the fluctuations in sequence composition of clone libraries resulted from cloning bias. Clonal SSU rRNA gene sequences were used to define operational taxonomic units (OTUs) for T-RFLP analysis, which were distinguished by group-specific TaqI restriction sites. Sequence analysis showed a high degree of conservation of TaqI restriction sites within the different archaeal lineages present in Italian rice field soil. Direct T-RFLP analysis of archaeal populations in rice field soil slurries revealed the presence of all archaeal lineages detected by cloning with a predominance of terminal restriction fragments characteristic of rice cluster I (389 bp), Methanosaetaceae (280 bp), and Methanosarcinaceae/rice cluster VI (182 bp). In general, the relative gene frequency of most detected OTUs remained rather constant over time during the first 17 days after flooding of the soil. Most minor OTUs (e.g., Methanomicrobiaceae and rice cluster III) and Methanosaetaceae did not change in relative frequency. Rice cluster I (37 to 30%) and to a lesser extent rice cluster IV as well as Methanobacteriaceae decreased over time. Only the relative abundance of Methanosarcinaceae (182 bp) increased, roughly doubling from 15 to 29% of total archaeal gene frequency within the first 11 days, which was positively correlated to the dynamics of acetate and formate concentrations. Our results indicate that a functionally dynamic ecosystem, a rice field soil after flooding, was linked to a relatively stable archaeal community structure.