Patterns of biotic community organization and reorganization: A conceptual framework and a case study

Reorganization is an important concept for confronting complex adaptive systems (CAS) theory with ecological reality. However, little work has been done to translate the reorganization idea into a practical conceptual framework. This paper focuses on community-level reorganization, the process of re-forming patterns in relation to the distribution of species density (abundance) and their frequency of occurrence in space (incidence). We assert that changes in species positions in the incidence–abundance (IA) phase plane depict community reorganization in response to environmental changes. This is because species positions in the IA plane represent the most prominent organizational features of a biotic community.We identified four sequential levels of species reorganization in the IA phase plane: reshuffling of species, species appearance, species disappearance and whole-assemblage shift. We propose that the sequential levels represent an increase in reorganization intensity depending on the extent of environmental change.We formulate the Environmental Change and Re-Organization (ECRO) hypothesis specifying that ecosystems respond predictably in terms of community reorganization in the IA phase plane to external drivers. The predictable reorganization follows the four sequential levels of organization in response to intensity of environmental change. We suggest that the response of a species assemblage to external drivers in sequential levels of reorganization is independent of ecosystem properties, type of environmental variables, taxa, and spatio-temporal scales.We tested the predictability of reorganization according to the ECRO hypothesis, using annual plant assemblages of a semiarid shrubland. These assemblages exhibit CAS properties as suggested by Levin: high species diversity, high numbers of individuals, local interactions among individuals in relation to water consumption, and annually selected species subsets for replication.We investigated annual plant assemblage organization and reorganization for 12 years in response to disturbance and resource input, using the IA phase plane. The field study supports our assertion that reorganization of species assemblages in response to environmental change can be represented by species repositioning in the IA phase plane, and that community reorganization follows the four sequential levels of reorganization in response to the intensity of environmental change.Our conceptual framework and experimental studies demonstrate that hypotheses related to core CAS concepts of organization and reorganization can be tested by linking them with community ecology concepts of species patterns in the IA phase plane. We also discuss the relationship between reorganization in the IA phase plane and resilience, regime shift and ecosystem functioning as affected by species response and effects traits.     

Role of MAP kinase and myosin light chain kinase in chromosome-induced development of mouse egg polarity

During maturation, the mouse oocyte is transformed into a highly polarized egg, characterized by an actin cap and cortical granule-free domain (CGFD) overlying the meiotic spindle that is in close proximity to the cortex. The presence of spindle/chromosomes or microinjected sperm chromatin in the cortical region initiates this cortical reorganization, but the pathway is unknown. We report that cortical reorganization induced by microinjected sperm chromatin is blocked by inhibitors of microfilament assembly or disassembly. Active mitogen-activated protein kinase (MAPK), which becomes enriched in the region of sperm chromatin, is required for cortical reorganization, because microinjected sperm chromatin fails to induce cortical reorganization in Mos-/- eggs, which lack MAPK activity. Last, myosin light chain kinase (MLCK), which can be directly phosphorylated and activated by MAPK, appears involved, because the MLCK inhibitors ML-7 and Peptide 18 prevent sperm chromatin-induced cortical reorganization. These results provide new insights into how cortical reorganization occurs independently of extracellular signals to generate egg polarity.     

The medium reorganization energy for the charge transfer reactions in proteins

A low static dielectric permittivity of proteins causes the low reorganization energies for the charge transfer reactions inside them. This reorganization energy does not depend on the pre-existing intraprotein electric field. The charge transferred inside the protein interacts with its aqueous surroundings; for many globular proteins, the effect of this surroundings on the reorganization energy is comparable with the effect of reorganization of the protein itself while for the charge transfer in the middle of membrane the aqueous phase plays a minor role. Reorganization energy depends strongly on the system considered, and hence there is no sense to speak on the "protein reorganization energy" as some permanent characteristic parameter. We employed a simple algorithm for calculation of the medium reorganization energy using the numerical solution of the Poisson-Boltzmann equation. Namely, the reaction field energy was computed in two versions - all media having optical dielectric permittivity, and all the media with the static one; the difference of these two quantities gives the reorganization energy. We have calculated reorganization energies for electron transfer in cytochrome c, various ammine-ruthenated cytochromes c, azurin, ferredoxin, cytochrome c oxidase, complex of methylamine dehydrogenase with amicyanin, and for proton transfer in α-chymotrypsin. It is shown that calculation of the medium reorganization energy can be a useful tool in analysis of the mechanisms of the charge transfer reactions in proteins.     

Morphallaxis in an aquatic oligochaete, Lumbriculus variegatus: reorganization of escape reflexes in regenerating body fragments

We describe functional and anatomical correlates of the reorganization of giant nerve fiber-mediated escape reflexes in body fragments of an aquatic oligochaete, Lumbriculus variegatus, a species that reproduces asexually by fragmentation. Since fragments from any axial position always regenerate short heads (seven or eight segments long) and much longer tail sections, segments originating from posterior fragments become transposed along the longitudinal axis and acquire, by morphallaxis, features of escape reflex organization that conform to their new anterior position. Using noninvasive electrophysiological recordings we have quantified, on a day-to-day and a segment-by-segment basis, the reorganization that occurs in sensory field arrangements of the medial (MGF) and lateral (LGF) giant nerve fibers, as well as changes in giant fiber conduction velocity and morphometry. Our results show that (1) posterior fragments, originally subserved by the LGF sensory field gradually become subserved by the MGF sensory field; (2) appropriate increases in the ratio of MGF:LGF cross-sectional area, perimeter, and conduction velocity accompany the reorganization in giant fiber sensory fields; and (3) sensory field reorganization can be repeatedly reversed by additional amputations. These results demonstrate that the functional organization of escape reflexes is highly plastic and that morphallaxis may result from the counterbalance of morphogenic influences localized within the anterior and posterior ends of regenerating body fragments.     

冠突伪尾柱虫有性生殖期间皮膜发育的核控制

通过显微手术去小核建立多个冠突伪尾柱虫（Pseudourostyla cristata)无小细胞系,并诱导它们与有小核细胞进行接合生殖,以评估小核及其衍生的大核原基在有性生殖期间对皮膜形态发生的影响,当无小核接合体从有小核配偶获得1枚配子核后,接合双方不仅能平行地继续核器演化,而且使第1次皮膜改组能够同步进行和正常发育,说明小核在有性周期中除了生殖功能外仍保留着某些控制皮膜发育的体功能,虽然大部分接合后体的大核原基在DNA贫乏期停止发育,但少数接合后体能够超越这一时期,并启动第2次皮膜改组和顺利完成其后续的有性发育全程,表明指令发动第2次皮膜发育的信号来自DNA贫乏期后以排出一核物质团块为标志的大核原基。     

Encoding strategies dissociate prefrontal activity from working memory demand

It is often proposed that prefrontal cortex is important in organization and control of working memory contents. In some cases, effective reorganization can decrease task difficulty, implying a dissociation between frontal activity and basic memory demand. In a spatial working memory task, we studied the improvement of performance that occurs when materials can be reorganized into higher level groups or chunks. Structured sequences, encouraging reorganization and chunking, were compared with unstructured sequences. Though structured sequences were easier to remember, event-related functional magnetic resonance imaging (fMRI) showed increased activation of lateral frontal cortex, in particular during memory encoding. The results show that, even when memory demand decreases, organization of working memory contents into higher level chunks is associated with increased prefrontal activity.     

Acceleration by NMDA treatment of visually induced map reorganization in juvenile Xenopus after larval eye rotation

Each tectal lobe of Xenopus forgs receives two topographic maps, one via the ipsilateral eye and one via the contralateral eye. The alignment of the ipsilateral map with the contralateral map depends upon bincoular visual input during a critical period that extends from late tadpole to early juvenile stages. Rotation of one eye during the critical period leads to reorganization of the ipsilateral map, which eventually comes back into alignment with the contralateral map despite the abnormal eye position. The ipsilateral eye's map initially develops as if there had been no alteration in eye position; there is a delay of 4–6 weeks before reorganization can be detected by electrophysiological mapping. In this paper, the possible role of the NMDA receptor in the delay in reorganization is addressed. The degree of NMDA receptor activation may need to be above some threshold level to trigger reorganization. If NMDA receptor activation normally is below that level until after the first month postmetamorphosis, then exogenous NMDA might boost the process sufficiently to start the reorganization process sooner than usual. In order to test this possibility, the left eye of tadpoles was rotated and NMDA was applied to the right tectal lobe for 3–5 weeks, starting at 1 week postmetamorphosis. Electrophysiological mapping demonstrated that reorganization takes place more rapidly than in untreated forgs or frogs treated with vehicle only. This result is consistent with the interpretation that the activation of the NMDA receptor is a rate-limiting step in the activity-dependent matching of binocular maps in Xenopus tectum. 1994 John Wiley & Sons, Inc.     

Commitment to the First Cortical Reorganization During Conjugation in Stylonychia mytilus: An Argument for Homology with Cortical Development During Binary Fission

The asexual nature of the first cortical reorganization of conjugation in Stylonychia was analyzed by comparing the effect of amputation performed at different stages of early conjugation to that performed on vegetative cells at different stages of the cell cycle. Amputation of vegetative cells delineated a point of commitment to binary fission at 0.51–0.57 of the cell cycle. Cells amputated before this point were induced to undergo the regenerative mode of asexual development, but those amputated after this point continued with binary fission. In parallel, during conjugation a similar commitment was made around the time of formation of tight mating-pairs: early conjugants amputated around this time might undergo regeneration, and those operated on after this stage continued with the first cortical reorganization as in typical conjugants. The two mates of a pair might differ in their response to amputation, suggesting that the timing of commitment to the first cortical reorganization is not related to the events of conjugation, but rather is individually determined in the vegetative cycle of the cells before they pair up in mating. These observations provide support for the notion that the first cortical reorganization of conjugants is homologous to the asexual mode of cortical development in dividers, according to the theory of developmental heterochrony in the sexual reproduction of hypotrichs. The timing of commitment to the first cortical reorganization was found to temporally correlate with the entrance of the micronuclei into meiosis. Since the first cortical reorganization can proceed without the micronucleus, this raises the possibility that initiation of micronuclear meiosis is closely coupled with, and may be determined by, the commitment to the first cortical reorganization.     

Chromatin reorganization during senescence of proliferating cells.

It was previously proposed (Macieira-Coelho, 1979) that aging of proliferating cells is the result of genome reorganization taking place during the division cycle. This hypothesis was investigated and a reorganization could indeed be ascertained in the different hierarchical orders of DNA structure; a correlation was found between changes in chromatin organization and the impairment of cell cycle-related events. Indeed, like the latter, the reorganization of chromatin structure is characterized by a succession of subtle changes through the cell population life span, and a final short stage with abrupt events. The final events seem to concern mainly the organization of heterochromatin. The reorganization in the genome is accompanied by structural changes in the cellular scaffold and an evolution of cell morphology. The remodeling occurring in the cell through serial divisions seems to take place in such a way as to decrease the probability of further reorganizations, tending to a limit. The decline of the proliferative activity seems to be the result of the tendency to reach this limit.     

Deoxyribonucleic Acid Synthesis and Distribution During Growth and Amitosis of the Macronucleus of Euplotes

SYNOPSIS. Short sections of deoxyribonucleic acid (DNA) in the elongated macronucleus of Euplotes eurystomus were labeled by means of a short exposure to tritiated (H³-) thymidine to follow by autoradiography the fate of the labeled DNA during amitotic reorganization of the macronucleus. During amitosis the radioactive DNA that was restricted during interphase to short sections of the nucleus is dispersed and becomes evenly distributed throughout each daughter macronucleus.
Although the reorganization bands normally originate only at the ends of the macronucleus, additional bands can start at other places on the macronuclear surface. Bands of the same macronucleus originate with a high degree of synchrony. DNA synthesis is a constant feature of the rear zone of every reorganization band.     

Role of F-actin organization in p38 MAP kinase-mediated apoptosis and necrosis in neonatal rat cardiomyocytes subjected to simulated ischemia and reoxygenation

Activation of p38 mitogen-activated protein (MAP) kinase (MAPK) has been implicated in the mechanism of cardiomyocyte (CMC) protection and injury. The p38 MAPK controversy may be related to differential effects of this kinase on apoptosis and necrosis. We have hypothesized that p38 MAPK-mediated F-actin reorganization promotes apoptotic cell death, whereas it protects from osmotic stress-induced necrotic cell death. Cultured neonatal rat CMCs were subjected to 2 h of simulated ischemia followed by reoxygenation. p38 MAPK activity measured by phosphorylation of MAP kinase-activated protein (MAPKAP) kinase 2 was increased during simulated ischemia and reoxygenation. This was associated with translocation of heat shock protein 27 (HSP27) from the cytosolic to the cytoskeletal fraction and F-actin reorganization. Cytochrome c release from mitochondria, caspase-3 activation, and DNA fragmentation were increased during reoxygenation. Robust lactate dehydrogenase (LDH) release was observed under hyposmotic (140 mosM) reoxygenation. The p38 MAPK inhibitor SB-203580 abrogated activation of p38 MAPK, translocation of HSP27, and F-actin reorganization and prevented cytochrome c release, caspase-3 activation, and DNA fragmentation. Conversely, SB-203580 enhanced LDH release during hyposmotic reoxygenation. The F-actin disrupting agent cytochalasin D inhibited F-actin reorganization and prevented cytochrome c release, caspase-3 activation, and DNA fragmentation, whereas it enhanced LDH release during hyposmotic reoxygenation. When CMCs were incubated under the isosmotic condition for the first 15 min of reoxygenation, SB-203580 and cytochalasin D increased ATP content of CMCs and prevented LDH release after the conversion to the hyposmotic condition. These results suggest that F-actin reorganization mediated by activation of p38 MAPK plays a differential role in apoptosis and protection against osmotic stress-induced necrosis during reoxygenation in neonatal rat CMCs; however, the sarcolemmal fragility caused by p38 MAPK inhibition can be reversed during temporary blockade of physical stress during reoxygenation.     

Morphological changes of the adipose cell plasma membrane during lipolysis

Morphological changes of the plasma membrane in the white adipose cell associated with lipid mobilization were assessed qualitatively and quantitatively on freeze-fracture replicas of epididymal adipose tissue from fasted and from streptozotocin-diabetic rats. The number of plasma membrane invaginations and intramembranous particles were evaluated per square micrometer of membrane and per entire adipocyte. These two determinations show that the number per square micrometer (local concentration) of both structural features progressively increases with the duration of diabetes and fasting, while that at the same time their number per entire cell (total content) remains unchanged. These data thus show: (a) a reorganization of the adipose cell plasma membrane during lipolysis; and (b) that this reorganization can be detected only by determining the concentration and the total content of the structural features of the membrane involved.     

The principles of data formalization for building the genetic-morphological model of shoot development in flowering plants

Shoot system of a plant can be divided into elementary molecules composed of phyllome, internode, and meristem of the lateral bud. The capacity of plants for open growth is manifested as multiple reproductions of the modules. These main principles of plant structural organization can be used to formalize and integrate the data from various disciplines studying the shoot development--genetics of development, morphology, etc. At the example of model species Arabidopsis thaliana we show that the data on genetic control of shoot development can be considered in terms of individual modules reorganization. Several variants of the modules structural reorganization are allowed: reduction or transformation of phyllome, change in the internode length, and triggering active/inactive status of the lateral shoot meristem. Each variant of the module structure corresponds to specific pattern of genes activity. Such integration of the data on genetic and structural aspects of morphogenesis can form a basis for mathematical modeling of plant development.     

Driving plasticity in human adult motor cortex is associated with improved motor function after brain injury

Changes in somatosensory input can remodel human cortical motor organization, yet the input characteristics that promote reorganization and their functional significance have not been explored. Here we show with transcranial magnetic stimulation that sensory-driven reorganization of human motor cortex is highly dependent upon the frequency, intensity, and duration of stimulus applied. Those patterns of input associated with enhanced excitability (5 Hz, 75% maximal tolerated intensity for 10 min) induce stronger cortical activation to fMRI. When applied to acutely dysphagic stroke patients, swallowing corticobulbar excitability is increased mainly in the undamaged hemisphere, being strongly correlated with an improvement in swallowing function. Thus, input to the human adult brain can be programmed to promote beneficial changes in neuroplasticity and function after cerebral injury.     

Reorganization of the Intact Somatosensory Cortex Immediately after Spinal Cord Injury

Sensory deafferentation produces extensive reorganization of the corresponding deafferented cortex. Little is known, however, about the role of the adjacent intact cortex in this reorganization. Here we show that a complete thoracic transection of the spinal cord immediately increases the responses of the intact forepaw cortex to forepaw stimuli (above the level of the lesion) in anesthetized rats. These increased forepaw responses were independent of the global changes in cortical state induced by the spinal cord transection described in our previous work (Aguilar et al., J Neurosci 2010), as the responses increased both when the cortex was in a silent state (down-state) or in an active state (up-state). The increased responses in the intact forepaw cortex correlated with increased responses in the deafferented hindpaw cortex, suggesting that they could represent different points of view of the same immediate state-independent functional reorganization of the primary somatosensory cortex after spinal cord injury. Collectively, the results of the present study and of our previous study suggest that both state-dependent and state-independent mechanisms can jointly contribute to cortical reorganization immediately after spinal cord injury.     

The modification of cortical reorganization and chronic pain by sensory feedback

Recent neuroscientific evidence has revealed that the adult brain is capable of substantial plastic change in areas such as the primary somatosensory cortex that were formerly thought to be modifiable only during early experience. We discuss research on phantom limb pain as well as chronic back pain that revealed functional reorganization in both the somatosensory and the motor system in these chronic pain states. In phantom limb pain patients, cortical reorganization is correlated with the amount of phantom limb pain; in low back pain patients the amount of reorganizational change increases with chronicity. We present a model of the development of chronic pain that assumes an important role of somatosensory pain memories. In phantom limb pain, we propose that those patients who experienced intense pain prior to the amputation will later likely develop enhanced cortical reorganization and phantom limb pain. We show that cortical plasticity related to chronic pain can be reduced by behavioral interventions that provide feedback to the brain areas that were altered by somatosensory pain memories.     

Sequestration of pRb by cyclin D3 causes intranuclear reorganization of lamin A/C during muscle cell differentiation

The A-type lamins that localize in nuclear domains termed lamin speckles are reorganized and antigenically masked specifically during myoblast differentiation. This rearrangement was observed to be linked to the myogenic program as lamin speckles, stained with monoclonal antibody (mAb) LA-2H10, were reorganized in MyoD-transfected fibroblasts induced to transdifferentiate to muscle cells. In C2C12 myoblasts, speckles were reorganized early during differentiation in cyclin D3-expressing cells. Ectopic cyclin D3 induced lamin reorganization in C2C12 myoblasts but not in other cell types. Experiments with adenovirus E1A protein that can bind to and segregate the retinoblastoma protein (pRb) indicated that pRb was essential for the cyclin D3-mediated reorganization of lamin speckles. Cyclin D3-expressing myoblasts displayed site-specific reduction of pRb phosphorylation. Furthermore, disruption of lamin structures by overexpression of lamins inhibited expression of the muscle regulatory factor myogenin. Our results suggest that the reorganization of internal lamins in muscle cells is mediated by key regulators of the muscle differentiation program.     

A Dynamical Model of Fast Cortical Reorganization

In this work we study the connection between some dynamic effects at the synaptic level and fast reorganization of cortical sensory maps. By using a biologically plausible computational model of the primary somatosensory system we obtained simulation results that can be used to relate the dynamics of the interactions of excitatory and inhibitory neurons to the process of somatotopic map reorganization immediately after peripheral lesion. The model consists of three regions integrated into a single structure: tactile receptors representing the glabrous surface of the hand, ventral posterior lateral nucleus of the thalamus and area 3b of the primary somatosensory cortex, reproducing the main aspects of the connectivity of these regions. By applying informational measures to the simulation results of the dynamic behavior of AMPA, NMDA and GABA synaptic conductances we draw some conjectures about how the several neuronal synaptic elements are related to the initial stage of the digit-induced reorganization of the hand map in the somatosensory cortex.