bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flooding and canopy dynamics shape the demography of a clonal Amazon understorey herb
Authors: Schleuning Matthias , Huamán Vicky , Matthies Diethart 
Published: July 2008

Summary

Tropical forests have highly diverse and often dense understorey vegetation. However, little is known about the demography of tropical understorey species and their response to common events like flooding and gap formation that change the prevailing environmental conditions.
We studied the influence of flooding and canopy gaps on the demography of the widespread clonal herb Heliconia metallica in 16 populations in the Peruvian Amazon over two wet and two dry seasons. In a factorial study design, we selected several populations in canopy gaps and under a closed canopy both at flooded and non‐flooded sites.
Using periodic matrix models, we determined projected population growth rates during seasonal and annual time intervals and applied prospective and retrospective analyses to identify the life cycle components that contributed most to the differences in annual growth rates among the four combinations of habitat conditions.
All populations increased in size during the wet and decreased during the dry season. In both years, projected annual growth rates of the non‐flooded populations were less than 1 both in gaps and under a closed canopy. In contrast, over the 2‐year study period growth rates of the flooded populations were close to 1 both in gaps and under a closed canopy.
The life history of H. metallica was dominated by ramet survival and clonal growth, whereas seedling recruitment was very rare. In canopy gaps, growth and clonal expansion were rapid and reproduction was frequent, whereas under a closed canopy ramets grew little and rarely flowered. Population decline at non‐flooded sites was due to higher ramet mortality during the dry season. However, the effects of flooding and canopy gaps interacted and affected life‐history components differently in wet and dry seasons and in successive years.
Synthesis. The intricate interacting effects of flooding and canopy gaps determine the population dynamics of the understorey herb H. metallica. The clonal life form and the plasticity of the ramets enable the populations to persist under variable light conditions, but may not be able to buffer the increasingly frequent periods of drought in Amazon forests.
Biological Flora of the British Isles: Primula elatior (L.) Hill
Authors: Taylor Kenneth , Woodell Stanley R. J. 
Published: July 2008

Summary

This account presents information on all aspects of the biology of Primula elatior that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, and conservation.
Primula elatior is a native perennial herb, within a compact area in the British Isles, in ancient woods and copses on the chalky boulder clay in East Anglia, where it is abundant locally although scarce nationally. British material is ssp. elatior, which extends across much of Europe, becoming rarer towards the south.
Primula elatior is a shade tolerant species, but only flowers in profusion in the increased light levels following tree felling in traditionally coppiced woods. It is confined to an area of the British Isles where the soils are seasonally waterlogged and ill‐aerated, and is very tolerant of the toxic levels of ferrous iron which accumulate in the surface horizons in the spring months. It has a poorly developed drought tolerance.
An early flowering plant, P. elatior is an insect‐pollinated obligate outbreeder, with two self‐incompatible morphs (pin and thrum). The low colonizing ability of this ancient woodland species can be attributed to both seed dispersal and seedling recruitment limitation.
There has been a steady reduction in the density of P. elatior in woodland sites during the past centuries. However, there has been little change in the 10‐km distribution in the British Isles. Studies of populations involve three groups of factors: genetic variation, environmental changes and population structure. Potentially these factors have a greater effect on small and isolated populations than on large and integrated ones. There is no evidence that the species suffers from a loss of genetic diversity in the smaller populations. Primula elatior seems to have a relatively high level of genetic diversity that is maintained despite a fragmented distribution.
Within its restricted distribution area P. elatior replaces P. vulgaris completely. At the margins of their distributions the two species occur together in a number of woodland sites, providing the opportunity for hybridization. As they are highly interfertile, hybridization is restricted mainly by differences in their habitat preferences. The hybrid P. vulgaris × P. elatior = P. × digenea is fertile and gives rise to hybrid swarms which are found in all British sites where both parents occur together.
Changes in climate, woodland management practices and intensities of deer grazing, especially by Fallow deer (Dama dama), are likely to have a major effect on populations of P. elatior. Since the species colonizes new or secondary woodlands very slowly, management should focus on the conservation of ancient semi‐natural woodlands.
Confocal imaging of glutathione redox potential in living plant cells
Authors: SCHWARZLÄNDER M. , FRICKER M.D. , MÜLLER C. , MARTY L. , BRACH T. , NOVAK J. , SWEETLOVE L.J. , HELL R. , MEYER A.J. 
Published: July 2008

SummaryReduction–oxidation‐sensitive green fluorescent protein (roGFP1 and roGFP2) were expressed in different sub‐cellular compartments of Arabidopsis and tobacco leaves to empirically determine their performance as ratiometric redox sensors for confocal imaging in planta. A lower redox‐dependent change in fluorescence in combination with reduced excitation efficiency at 488 nm resulted in a significantly lower dynamic range of roGFP1 than for roGFP2. Nevertheless, when targeted to the cytosol and mitochondria of Arabidopsis leaves both roGFPs consistently indicated redox potentials of about –320 mV in the cytosol and –360 mV in the mitochondria after pH correction for the more alkaline matrix pH. Ratio measurements were consistent throughout the epidermal cell layer, but results might be attenuated deeper within the leaf tissue. Specific interaction of both roGFPs with glutaredoxin in vitro strongly suggests that in situ both variants preferentially act as sensors for the glutathione redox potential. roGFP2 targeted to plastids and peroxisomes in epidermal cells of tobacco leaves was slightly less reduced than in other plasmatic compartments, but still indicated a highly reduced glutathione pool. The only oxidizing compartment was the lumen of the endoplasmic reticulum, in which roGFP2 was almost completely oxidized. In all compartments tested, roGFP2 reversibly responded to perfusion with H2O2 and DTT, further emphasizing that roGFP2 is a reliable probe for dynamic redox imaging in planta. Reliability of roGFP1 measurements might be obscured though in extended time courses as it was observed that intense irradiation of roGFP1 at 405 nm can lead to progressive photoisomerization and thus a redox‐independent change of fluorescence excitation ratios.
Sphere size distributions from finite thickness sections: a forward approach employing a genetic algorithm
Authors: DE NOOIJER S. , KETELAAR T. , MULDER B. 
Published: July 2008

SummaryWe formulate, implement and test a robust method of determining sphere size distributions from finite thickness planar sections. The method uses a forward approach in which populations of proposed distributions are tested against the input data and refined using a genetic algorithm. This method is then applied to a real‐world data set concerning endo‐ and exocytotic vesicles in the apical region of tip growing pollen tubes of Arabidopsis thaliana.
Cellulose microfibril deposition: coordinated activity at the plant plasma membrane
Authors: LINDEBOOM J. , MULDER B.M. , VOS J.W. , KETELAAR T. , EMONS A.M.C. 
Published: July 2008

SummaryPlant cell wall production is a membrane‐bound process. Cell walls are composed of cellulose microfibrils, embedded inside a matrix of other polysaccharides and glycoproteins. The cell wall matrix is extruded into the existing cell wall by exocytosis. This same process also inserts the cellulose synthase complexes into the plasma membrane. These complexes, the nanomachines that produce the cellulose microfibrils, move inside the plasma membrane leaving the cellulose microfibrils in their wake. Cellulose microfibril angle is an important determinant of cell development and of tissue properties and as such relevant for the industrial use of plant material. Here, we provide an integrated view of the events taking place in the not more than 100 nm deep area in and around the plasma membrane, correlating recent results provided by the distinct field of plant cell biology. We discuss the coordinated activities of exocytosis, endocytosis, and movement of cellulose synthase complexes while producing cellulose microfibrils and the link of these processes to the cortical microtubules.
Having a swell time – mitochondrial morphology and plant cell death programmes
Authors: LOGAN D.C. 
Published: July 2008

SummaryCell death is a vital process in multi‐cellular eukaryotes. Rather than being a contradiction in terms, this statement highlights the importance of limited and localized cell killing to the health and normal development of complex organisms. The main focus of this article is the role of mitochondrial morphological changes during cell death programmes, and the conserved role of mitochondrial permeability transition (increased permeability of either the outer or inner membrane) as an early mechanistic event preceding cell death in both plant and non‐plant eukaryotes. A second focus of this article is a review of the terminology and fundamental paradigms underpinning cell death research. Because of the importance of the process of cell death, there has been an enormous quantity of research performed to try to understand the underlying biological mechanisms. One result of such a large and varied research effort, and a result that is perhaps particularly evident to investigators coming into the field anew, is that some of the basic tenets of cell death research appear to have become confused. In this short article, I make an attempt to clarify the subject, focussing on the role of mitochondria, and the difficulties in comprehensibility arising from the sometimes‐erroneous, or at least unnecessarily confusing use of specific terminology; there are several key terms in the cell death literature that appear interchangeable when they are not, or are interchanged when they should not be.
Going green: plants' alternative way to position the Ran gradient
Authors: MEIER I. , XU X.M. , BRKLJACIC J. , ZHAO Q. , WANG H.‐J. 
Published: July 2008

SummaryRan is a multi‐functional small GTPase of the Ras super‐family involved in nucleocytoplasmic transport, mitotic spindle assembly, cell cycle control and nuclear envelope (NE) formation. Its roles are accomplished by the asymmetric distribution of its GTP‐ and GDP‐bound forms, enabled by the specific localization of Ran accessory proteins, the Ran GTPase‐activating protein RanGAP and the nucleotide exchange factor RCC1. Mammalian RanGAP1 is targeted to the NE during interphase and to the spindle and kinetochores during mitosis via a SUMOylated C‐terminal domain and interaction with the nucleoporin Nup358/RanBP2. Arabidopsis RanGAP1 (AtRanGAP1) lacks the SUMOylated C‐terminal domain of vertebrate RanGAP, but contains a plant‐specific N‐terminal domain (WPP domain), which is necessary and sufficient for its targeting to the NE in interphase. AtRanGAP1 has a mitotic trafficking pattern uniquely different from that of vertebrate RanGAP, which includes targeting to the outward‐growing rim of the cell plate. The WPP domain is necessary and sufficient for this targeting. Now, a novel family of plant‐specific, nuclear pore‐associated proteins has been identified in Arabidopsis, which is essential for anchoring RanGAP to the Arabidopsis nuclear envelope at the root meristem. This suggests that RanGAP anchoring to the nuclear pore has been solved in two fundamentally different ways in animals and plants. These findings support a separate evolution of RanGAP targeting mechanisms in different kingdoms, possibly related to different functional geometries of the Ran gradient in animal and higher plant cell division.
Functions, regulation and cellular localization of plant cyclin‐dependent kinase inhibitors
Authors: WANG H. , ZHOU Y. , BIRD D.A. , FOWKE L.C. 
Published: July 2008

SummaryThe cell cycle is regulated by the cyclin‐dependent kinase (CDK), and CDK inhibitors can bind to CDKs and inhibit their activities. This review examines plant CDK inhibitors, with particular emphasis on their molecular and cellular functions, regulation and cellular localization. In plants, a family of ICK/KRP CDK inhibitors represented by ICK1 is known and another type of CDK inhibitor represented by the SIMESE (SIM) has recently been reported. Considerable understanding has been gained with the ICK/KRP CDK inhibitors. These plant CDK inhibitors share only limited sequence similarity in the C‐terminal region with the KIP/CIP family of mammalian CDK inhibitors. The ICK/KRP CDK inhibitors thus provide good tools to understand the basic machinery as well as the unique aspects of the plant cell cycle. The ICK/KRP CDK inhibitors interact with D‐type cyclins or A‐type CDKs or both. Several functional regions and motifs have been identified in ICK1 for CDK inhibition, nuclear localization and protein instability. Clear evidence shows that ICK/KRP proteins are important for the cell cycle and endoreduplication. Preliminary evidence suggests that they may also be involved in cell differentiation and cell death. Results so far show that plant CDK inhibitors are exclusively localized in the nucleus. The molecular sequences regulating the localization and functional significance will be discussed.
Microinjecting FM4–64 validates it as a marker of the endocytic pathway in plants
Authors: Van GISBERGEN P.A.C. , ESSELING‐OZDOBA A. , VOS J.W. 
Published: July 2008

SummaryThe amphiphilic dye FM4–64 is used to investigate endocytosis and vesicle trafficking in living eukaryotic cells. The standing hypothesis is that it is inserted into the outer leaflet of the plasma membrane and, from there, is passed on to intracellular membrane compartments by endocytosis. We tested this hypothesis by microinjecting FM4–64 into the cytoplasm and vacuole of Nicotiana tabacum BY‐2 suspension culture cells and Tradescantia virginiana stamen hair cells. We found that the dye did not label any membranes when injected into the cytoplasm, but clearly labelled the tonoplast when injected directly into the vacuole. However, because the dye is pH‐sensitive, the fluorescence intensity between the plasma membrane and tonoplast varied. We conclude that FM4–64 is a specific marker for the endocytic pathway. Nevertheless, little is known about the molecular interactions of FM4–64 with these particular phospholipid membrane leaflets. We, therefore, appeal for biochemical research to determine which membrane lipids FM4–64 interacts with.
FRET analysis of transmembrane flipping of FM4–64 in plant cells: is FM4–64 a robust marker for endocytosis?
Authors: GRIFFING L. R. 
Published: July 2008

SummaryAlthough the styryl dye FM4–64 is now used routinely to monitor endocytosis in plants, the argument about its potential to cytoplasmically and non‐endocytically relocate into a selective set of vesicular compartments persists. To address this question, we determined whether fluorescence resonance energy transfer (FRET) could occur between a cytoplasmically expressed, short‐wavelength excitation green fluorescent protein (GFP) and FM4–64 in Nicotiana benthaminana. After exposure to FM4–64, the root hair plasma membrane and internal organelles became labelled. Under these conditions, no FRET with cytoplasmic GFP was seen. However, if the cells were treated with a low concentration of quillajasaponin, a membrane permeabilization agent, the cells continued to stream and FRET was detected. Thereby, we demonstrate that under conditions that do not severely compromise cell viability, the FM4–64 dye becomes a suitable FRET partner for the cytoplasmically localized GFP. Under normal conditions, FM4–64 does not significantly enter the cytosolic side of the membrane, but remains at the plasma membrane or trapped in the organelles of the endocytic pathway. Hence, when the structure or permeability of the plasma membrane is unaltered, FM4–64 dye is a robust marker for endocytosis.
Imaging complex nutrient dynamics in mycelial networks
Authors: FRICKER M.D. , LEE J.A. , BEBBER D.P. , TLALKA M. , HYNES J. , DARRAH P.R. , WATKINSON S.C. , BODDY L. 
Published: July 2008

SummaryTransport networks are vital components of multi‐cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi‐cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three‐dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time‐lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion‐based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon‐counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N‐transport phenomena, including rapid, preferential N‐resource allocation to C‐rich sinks, induction of simultaneous bi‐directional transport, abrupt switching between different pre‐existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier techniques shows that as the colony forms, it self‐organizes into well demarcated domains that are identifiable by differences in the phase relationship of the pulses. On the centimetre to metre scale, we have begun to use techniques borrowed from graph theory to characterize the development and dynamics of the network, and used these abstracted network models to predict the transport characteristics, resilience, and cost of the network.
Treatment outcomes of hepatic and pulmonary metastases from colorectal carcinoma
Authors: Lee Won‐Suk , Yun Hae‐Ran , Yun Seong‐Hyeon , Chun Ho‐Kyung , Lee Woo‐Yong , Kim Sung‐Joo , Choi Seong‐Ho , Heo Jin‐Seok , Joh Jae‐Won , Park Young‐Suk , Kang Won‐Ki 
Published: July 2008

AbstractBackground and Aim:  The resection of synchronous or metachronous pulmonary and liver metastasis is an aggressive treatment option for patients with stage IV colorectal cancer and has been shown to yield acceptable long‐term survival. We reviewed our experience with colorectal cancer patients with both liver and lung resections to determine the efficacy of surgical resections.Methods:  We performed a single institution, retrospective analysis of all patients who underwent surgical hepatic and pulmonary resection for metastatic colorectal cancer between 1995 and 2004.Results:  A total of 32 patients underwent resection of both hepatic and pulmonary metastases secondary to colorectal cancer. The 5‐year overall survival from initial operation was 60.8%. The disease‐free interval was 44.3 months (95% confidence interval: 24.7 and 63.8, respectively). Neither the number of pulmonary lesions nor the time interval between the primary surgery and the metastasectomy had a significant impact on survival (P = 0.134).Conclusion:  An aggressive surgical treatment of selected colorectal cancer patients with lung and liver metastases resulted in prolonged survival. The 5‐year survival rate of 60.8% with no perioperative mortality was observed in our study.
Liposome‐mediated gene transfer of endothelial nitric oxide synthase to cirrhotic rat liver decreases intrahepatic vascular resistance
Authors: Zhang Zhi‐Qi , Qiu Jiang‐Feng , Luo Meng , Sun Yong‐Wei , Zhao Gang , Chen Wei , Liu Hua , Wu Zhi‐Yong 
Published: July 2008

AbstractBackground and Aims:  Nitric oxide (NO) production by endothelial nitric oxide synthase (eNOS) in sinusoidal endothelial cells is reduced in the injured liver and leads to intrahepatic portal hypertension. The present study evaluates the effects of liposome‐mediated gene transfer of eNOS on the intrahepatic vascular resistance and portal venous pressure (PVP) in cirrhotic rats.Methods:  Hepatic cirrhosis was induced in male Sprague–Dawley rats by intraperitoneal injection of carbon tetrachloride (CCl4), whereas the control normal rats were given the same dose of peanut oil. Plasmid eukaryotic expression vector (liposome‐pcDNA3/eNOS) was injected into the portal vein of CCl4 cirrhotic rats, whereas cirrhotic controls received the same dose of naked plasmid (liposome‐pcDNA3) or Tris buffer, and control normal rats received the same dose of Tris buffer. Five days after gene transfer, the levels of eNOS mRNA and protein, NO production, PVP and the changes of hepatic intrahepatic vascular resistance were investigated.Results:  Five days after eNOS gene transfer, the levels of eNOS mRNA, eNOS protein and NO production in cirrhotic rats increased remarkably, while hepatic vascular resistance and PVP decreased significantly in cirrhotic rats.Conclusion:  Liposome‐mediated eNOS gene transfer via intraportal injection is feasible and the increase of intrahepatic eNOS leads to a marked decrease in introhepatic vascular resistance and PVP. These data indicate that intrahepatic eNOS plays an important role in the pathogenesis of portal hypertension and gene transfer of eNOS is a potential and novel therapy for portal hypertension.