Models for the length distributions of actin filaments: I. Simple polymerization and fragmentation

We studied mathematical models for the length distributions of actin filaments under the effects of polymerization/depolymerization, and fragmentation. In this paper, we emphasize the effects of these two processes acting alone. In this case, simple discrete and continuous models can be derived and solved explicitly (in several special cases), making the problem interesting from a modeling and pedagogical point of view. In a companion paper (Ermentrout and Edelstein-Keshet, 1998, Bull. Math. Biol. 60, 477–503) we investigate what happens when the processes act together, with particular attention to fragmentation by gelsolin, and with a greater level of biological detail.     

Hippo signaling,actin polymerization,and follicle activation in fragmented human ovarian cortex

The Hippo pathway has been associated with regulation of early follicle growth. Studies of murine ovaries suggest that changes in the actin cytoskeleton, caused by fragmentation, result in inhibition of the Hippo pathway, and in turn, may activate follicle growth. In humans, the connections between fragmentation, the actin cytoskeleton, and follicle activation are yet to be confirmed. In this study, we investigated the impact in vitro fragmentation of a human ovarian cortex on (a) actin polymerization, (b) components of the Hippo pathway, and (c) follicle growth in vivo. The results showed that the ratio between globular and filamentous actin remained unchanged at all timepoints (0, 10, 30, 60, 120, and 240 min) following tissue fragmentation. Neither was the Hippo pathway effector protein YES‐associated protein upregulated nor was gene expression of the downstream growth factors CCN2, CCN3, or CCN5 increased at any timepoint in the fragmented cortex. Furthermore, the number of growing follicles was similar in fragmented and intact cortex pieces after 6 weeks' xenotransplantation. However, the total number of surviving follicles was considerably lower in the fragmented cortex compared with intact tissue, suggesting detrimental effects of fragmentation on tissue grafting. These results indicate that fragmentation is likely to be ineffective to activate follicle growth in the human ovarian cortex.     

超高效液相色谱与串联四级杆飞行时间质谱仪联用技术结合质谱裂解规律快速分析Alternaria panax中二酮哌嗪类化学成分

【目的】利用超高效液相色谱与串联四级杆飞行时间质谱仪联用技术(ultra-high-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry,UPLC-Q-TOF-MS/MS)结合质谱裂解规律分析,靶向分离Alternaria panax发酵液粗提物中次生代谢产物。【方法】用马铃薯葡萄糖(potato dextrose broth,PDB)培养基液体发酵A.panax 14 d,将滤液用乙酸乙酯萃取后减压浓缩得粗提物;基于UPLC-Q-TOF-MS/MS方法(高分辨质谱、分子式与碎片峰等)分析粗提物化学成分及质谱裂解规律;采用半制备高效液相色谱(high-performance liquid chromatography,HPLC)方法进一步分离纯化;结合核磁共振波谱(nuclear magnetic resonance,NMR)和质谱(mass spectrometry,MS)等谱学技术以及与文献数据对照确定化合物结构。【结果】利用UPLC-Q-TOF-MS/MS技术分析出...     

Oryza sativa actin‐interacting protein 1 is required for rice growth by promoting actin turnover

Rapid actin turnover is essential for numerous actin‐based processes. However, how it is precisely regulated remains poorly understood. Actin‐interacting protein 1 (AIP1) has been shown to be an important factor by acting coordinately with actin‐depolymerizing factor (ADF)/cofilin in promoting actin depolymerization, the rate‐limiting factor in actin turnover. However, the molecular mechanism by which AIP1 promotes actin turnover remains largely unknown in plants. Here, we provide a demonstration that AIP1 promotes actin turnover, which is required for optimal growth of rice plants. Specific down‐regulation of OsAIP1 increased the level of filamentous actin and reduced actin turnover, whereas over‐expression of OsAIP1 induced fragmentation and depolymerization of actin filaments and enhanced actin turnover. In vitro biochemical characterization showed that, although OsAIP1 alone does not affect actin dynamics, it enhances ADF‐mediated actin depolymerization. It also caps the filament barbed end in the presence of ADF, but the capping activity is not required for their coordinated action. Real‐time visualization of single filament dynamics showed that OsAIP1 enhanced ADF‐mediated severing and dissociation of pointed end subunits. Consistent with this, the filament severing frequency and subunit off‐rate were enhanced in OsAIP1 over‐expressors but decreased in RNAi protoplasts. Importantly, OsAIP1 acts coordinately with ADF and profilin to induce massive net actin depolymerization, indicating that AIP1 plays a major role in the turnover of actin, which is required to optimize F‐actin levels in plants.     

Homocysteine inhibits store-mediated calcium entry in human endothelial cells: Evidence for involvement of membrane potential and actin cytoskeleton

The role of homocysteine for store-operated calcium influx was investigated in human umbilical cord endothelial cell line. Homocysteine significantly decreased thapsigargin-evoked Ca²⁺ entry, membrane hyperpolarization and actin polymerization. GSH and DTT prevented homocysteine-induced inhibition of thapsigargin-evoked Ca²⁺ entry, membrane hyperpolarization and actin polymerization; while GSSG had the opposite effect. Homocysteine blocked large conductance Ca²⁺-activated K⁺ (BK_Ca) channels in a concentration-dependent manner and related to the redox status of the endothelial cells. BK_Ca channels opener NS1619 reversed thapsigargin-evoked Ca²⁺ entry, membrane hyperpolarization and actin polymerization; BK_Ca channels inhibitor iberiotoxin had the opposite effect. The findings suggest that homocysteine is involved in store-regulated Ca²⁺ entry through membrane potential-dependent and actin cytoskeleton-dependent mechanisms, redox status of homocysteine and BK_Ca channels may play a regulatory role in it. (Mol Cell Biochem 269: 37–47, 2005)     

Organization of actin filaments in regenerating and outgrowing subprotoplasts from pollen tubes ofNicotiana tabacum L.

The dynamics of actin-filament organization in pollen-tube subprotoplasts ofNicotiana tabacum L. cv. Samsun during regeneration and outgrowth was examined using phalloidin probes and a non-fixation method. A succession of actin arrays was examined during subprotoplast regeneration that strongly resembled the actin dynamics described for developing microspores by Van Lammeren et al. (1989, Planta178, 531–539) and activated pollen by Tiwari and Polito (1988, Protoplasma147, 5–15). At the end of the succession the actin filaments often became extended between two opposite polar foci. The ordering of the cortical actin filaments reflected a polarity in the subprotoplasts which determined the plane of outgrowth. The site of outgrowth was often marked by a ring of actin filaments. As growth proceeded and tube-like structures were formed, the arrangement of cortical actin filaments was found to be transverse to the elongation axis. Since the patterns of actin distribution were identical in both caryoplasts and cytoplasts, it was concluded that the pollen-tube cytoplasm has the intrinsic capacity of reorganizing actin filaments and imposing polarity on the spherical subprotoplasts.     

Evolution of the Germline Actin Gene in Hypotrichous Ciliates: Multiple Nonscrambled IESs at Extremely Conserved Locations in Two Urostylids

In hypotrichous ciliates, macronuclear chromosomes are gene‐sized, and micronuclear genes contain short, noncoding internal eliminated segments (IESs) as well as macronuclear‐destined segments (MDSs). In the present study, we characterized the complete macronuclear gene and two to three types of micronuclear actin genes of two urostylid species, i.e. Pseudokeronopsis rubra and Uroleptopsis citrina. Our results show that (1) the gain/loss of IES happens frequently in the subclass Hypotrichia (formerly Stichotrichia), and high fragmentation of germline genes does not imply for gene scrambling; and (2) the micronuclear actin gene is scrambled in the order Sporadotrichida but nonscrambled in the orders Urostylida and Stichotrichida, indicating the independent evolution of MIC‐actin gene patterns in different orders of hypotrichs; (3) locations of MDS–IES junctions of micronuclear actin gene in coding regions are conserved among closely related species.     

Oxidation of glycosaminoglycans by free radicals and reactive oxidative species: A review of investigative methods

Abstract

Glycosaminoglycans, in particular hyaluronan (HA), and proteoglycans are components of the extracellular matrix (ECM). The ECM plays a key role in the regulation of cellular behaviour and alterations to it can modulate both the development of human diseases as well as controlling normal biochemical processes such as cell signalling and pro-inflammatory responses. For these reasons, in vitro fragmentation studies of glycosaminoglycans by free radicals and oxidative species are seen to be relevant to the understanding of in vivo studies of damage to the ECM. A wide range of investigative techniques have therefore been applied to gain insights into the relative fragmentation effects of several reactive oxidative species with the ultimate goal of determining mechanisms of fragmentation at the molecular level. These methods are reviewed here.     

Community assembly after long-term fragmentation: a case study of tropical rainforest in Xishuangbanna,south-west China

Background: Tropical rainforests represent the most species-rich and at the same time the most fragmented terrestrial biome on Earth. Fragmentation of tropical rainforests is having wide-ranging consequences for the maintenance of local species diversity and community assembly patterns.

Aims: To examine floristic changes and changes in community phylogenetic structure in the forest fragment over the past five decades.

Methods: A new taxonomic diversity algorithm (within-family diversity) was developed to assess floristic changes in the forest fragment. Community phylogenetic structure was then compared before and after fragmentation.

Results: Taxonomic diversity changed greatly among families, with changes occurring randomly across the phylogeny. The forest fragment had higher phylogenetic diversity, higher mean pair-wise phylogenetic distance, but lower mean nearest-neighbour distance. The community phylogenetic structure has changed significantly from clustering to dispersion.

Conclusions: High species turnover occurred in the forest fragment. While shade-tolerant species have been lost, and ruderal and alien species have been added, overall phylogenetic diversity has increased with species being more phylogenetically distant. Competitive exclusion, which was related to the relatively drier conditions in the forest after fragmentation, led the plant community phylogenetic structure to be more dispersed.     

Cortical actin filaments fragment and aggregate to form chloroplast-associated and free F-actin rings in mechanically isolatedZinnia mesophyll cells

Summary Changes in F-actin organization following mechanical isolation ofZinnia mesophyll cells were documented by rhodamine-phalloidin staining. Immediately after isolation, most cells contained irregular cortical actin fragments of varying lengths, and less than 5% of cells contained intact cortical filaments. During the first 8 h of culture, filament fragments were replaced by actin rings, stellate actin aggregates, and bundled filament fragments. Some of these aggregates had no association with organelles (free actin aggregates). Other aggregates were associated with chloroplasts, which changed in shape and location at the same time actin aggregates appeared. F-actin was concentrated within or around the nucleus in a small percentage of cells. After 12 h in culture, the percentage of cells with free actin rings and chloroplast-associated actin aggregates began to decline and the percentage of cells having intact cortical actin filaments increased greatly. Intermediate images were recorded that strongly indicate that free actin rings, chloroplast-associated actin rings, and other actin aggregates self-assemble by successive bundling of actin filament fragments. The fragmentation and bundling of F-actin observed in mechanically isolatedZinnia cells resembles changes in F-actin distribution reported after diverse forms of cell disturbance and appears to be an example of a generalized response of the actin cytoskeleton to cell stress.Abbreviations FITC fluorescein isothiocyanate - MBS m-maleimidobenzoic acid N-hydroxysuccinimide ester - RhPh tetramethylrhodamine isothiocyanate-phalloidin     

Food limitation of asexual reproduction in a spionid polychaete

Summary

The rate of asexual fragmentation in the spionid polychaete Pygospio elegans is shown to increase in the presence of augmented food levels and is a density-dependent response. Asexual reproduction does not occur when the animals are reproducing sexually.     

An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments

We report on an advanced universal Monte Carlo simulation model of actin polymerization processes offering a broad application panel. The model integrates major actin-related reactions, such as assembly of actin nuclei, association/dissociation of monomers to filament ends, ATP-hydrolysis via ADP-Pi formation and ADP-ATP exchange, filament branching, fragmentation and annealing or the effects of regulatory proteins. Importantly, these reactions are linked to information on the nucleotide state of actin subunits in filaments (ATP hydrolysis) and the distribution of actin filament lengths. The developed stochastic simulation modelling schemes were validated on: i) synthetic theoretical data generated by a deterministic model and ii) sets of our and published experimental data obtained from fluorescence pyrene-actin experiments. Build on an open-architecture principle, the designed model can be extended for predictive evaluation of the activities of other actin-interacting proteins and can be applied for the analysis of experimental pyrene actin-based or fluorescence microscopy data. We provide a user-friendly, free software package ActinSimChem that integrates the implemented simulation algorithms and that is made available to the scientific community for modelling in silico any specific actin-polymerization system.     

红树林源白骨壤链霉菌中多环稠合大环内酰胺类化合物的结构多样性研究

【目的】通过基因组挖掘的方法,研究红树林来源白骨壤链霉菌Streptomyces avicenniae 9-9中多环稠合大环内酰胺(PTMs)类化合物的结构多样性。【方法】通过生物信息学分析白骨壤链霉菌基因组序列,寻找PTMs类化合物的生物合成相关基因;利用UPLC-MS/MS技术对该菌的次级代谢产物进行分析。【结果】在白骨壤链霉菌基因组中发现PTMs生物合成基因簇(aviA-D);从菌液提取物中鉴定出5个PTMs类化合物,其中包括ikarugamycin(化合物1)和capsimycin B(化合物2);基于PTMs类化合物5-6-5环类型的MS/MS碎裂规律,对化合物3–5的结构进行了推测。【结论】红树林来源白骨壤链霉菌S.avicenniae 9-9具有产生5-6-5环类型的PTMs类化合物的能力。     

Inhibition of Glycolate Oxidase by Fatty Acids

Gelatin, soy protein, lysozyme, succinyl-casein and succinyl-egg albumin were allowed to react with methyl linoleate (ML) at a relative humidity (RH) of 0% at 50°C for 7 days (protein: ML = 1:1). Gel filtration indicated that only gelatin was extensively fragmented. The gelatin was then incubated with ML under various conditions, and changes in the molecular sizes, the gel forming abilities and the chemical characteristics were investigated. The fragmentation of gelatin was increased by decreasing the RH and with the increase in the ratio of ML to protein. The melting point of gel in heating and cooling gelatin was decreased by increasing the fragmentation. The contents of amide and carbonyl groups increased and that of amino group decreased as the reaction progressed at RH 0%, but no change in C-terminal amino acids was observed. Following the reaction at RH 0%, many kinds of amino acid residues of gelatin were damaged, although in our previous paper [Matoba et al.,Agric. Biol. Chem. , 46, 979 (1982)] such was not detected in casein and egg albumin. From the above results, we conclude that gelatin is susceptible to fragmentation by reaction with oxidizing lipids and one possible mechanism of the degradation may be the –N–C– scission of peptide bonds as proposed by Zirlin and Karel [J. Food Sci., 34, 160 (1969)]. Complex reactions other than this scission may also occur.     

Reviewing the potential for including habitat fragmentation to improve life cycle impact assessments for land use impacts on biodiversity

Purpose

The biosphere is progressively subjected to a variety of pressures resulting from anthropogenic activities. Habitat conversion, resulting from anthropogenic land use, is considered the dominant factor driving terrestrial biodiversity loss. Hence, adequate modelling of land use impacts on biodiversity in decision-support tools, like life cycle assessment (LCA), is a priority. State-of-the-art life cycle impact assessment (LCIA) characterisation models for land use impacts on biodiversity translate natural habitat transformation and occupation into biodiversity impacts. However, the currently available models predominantly focus on total habitat loss and ignore the spatial configuration of the landscape. That is, habitat fragmentation effects are ignored in current LCIAs with the exception of one recently developed method.

Methods

Here, we review how habitat fragmentation may affect biodiversity. In addition, we investigate how land use impacts on biodiversity are currently modelled in LCIA and how missing fragmentation impacts can influence the LCIA model results. Finally, we discuss fragmentation literature to evaluate possible methods to include habitat fragmentation into advanced characterisation models.

Results and discussion

We found support in available ecological literature for the notion that habitat fragmentation is a relevant factor when assessing biodiversity loss. Moreover, there are models that capture fragmentation effects on biodiversity that have the potential to be incorporated into current LCIA characterisation models.

Conclusions and recommendations

To enhance the credibility of LCA biodiversity assessments, we suggest that available fragmentation models are adapted, expanded and subsequently incorporated into advanced LCIA characterisation models and promote further efforts to capture the remaining fragmentation effects in LCIA characterisation models.

     

Purification and functional characterization of an 85-kDa gelsolin from the ascidians Microcosmus sulcatus and Phallusia mammilata

From the pharyngeal baskets of the ascidians Microcosmus sulcatus and Phallusia mammilata we have purified an 85-kDa protein that is characterized as a member of the gelsolin family. These proteins from both species show the same behaviour in functional assays. The ascidian gelsolin binds two actin monomers in a highly cooperative manner. This complex formation is Ca²⁺-dependent, but not completely reversible, as on removal of Ca²⁺ one actin monomer dissociates leaving a 1:1 complex between gelsolin and G-actin. The properties of F-actin severing and G-actin nucleation depend on the presence of free Ca²⁺ in a micromolar range, with half maximum activation at about 3×10⁻⁶ M. The protein becomes inactivated when Ca²⁺ concentrations of 0.5 mM are exceeded. Fragmentation of F-actin by the ascidian gelsolin is comparably fast to that of vertebrate gelsolin. A steady state of actin fragmentation is reached within 2–4 s. Promotion of G-actin nucleation is also comparable to that of vertebrate gelsolin. Regarding functional aspects, the ascidian gelsolin is more closely related to vertebrate gelsolin than to an arthropod gelsolin from crayfish tail muscle.     

Poly(a)+ rna during vegetative development ofacetabularia peniculus

Summary In the juvenile stage, the diploid giant-celled green algae Acetabularia spp. are differentiated into an upright stalk and an irregularly branched rhizoid. Early amputation and grafting experiments as well as biochemical and molecular analyses have shown that mRNA (as poly(A)⁺ RNA) is continuously supplied from the primary nucleus in the rhizoid and accumulates in the stalk apex. In the present study, localization of poly(A)⁺ RNA in the juvenile stage of theAcetabularia peniculus was investigated by fluorescent in situ hybridization using oligo(dT) as a probe. The signal was localized in the apical cytoplasm and, in addition, multiple longitudinal striations throughout the stalk and rhizoid cytoplasm. A large portion of the poly(A)⁺ RNA striations exhibited structural polarity, broadened at one end and gradually thinned toward the other end. Some of the striations in the rhizoid cytoplasm were continuous with a zone of signal in the area of the perinuclear rim. The poly(A)⁺ RNA striations were associated with thick bands of longitudinal actin bundles which run through the entire length of the stalk. Cytochalasin D caused fragmentation of the actin bundles and irregular distribution of the fluorescent signal. We suggest that the poly(A)⁺ RNA striations constitute a hitherto unknown form of packaged mRNA that is transported over large distances along the actin cytoskeleton to be stored and expressed in the growing apex.     

Mechanisms of the modulation of actin-myosin interactions by A1-type myosin light chains

BackgroundThe interaction of N-terminal extension of the myosin A1 essential light chain (A1 ELC) with actin is receiving increasing attention as a target in utilizing synthetic A1 ELC N-terminal-derived peptides in cardiac dysfunction therapy.MethodsTo elucidate the mechanism by which these peptides regulate actin-myosin interaction, here we have investigated their effects on the myosin subfragment 1 (S1)-induced polymerization of G-actin.ResultsThe MLCF_pep and MLCS_pep peptides spanning the 3–12 of A1 ELC sequences from fast and slow skeletal muscle, respectively, increased the rate of actin polymerization not only by S1(A2) but also the rate of S1(A1)-induced actin polymerization, suggesting that they did not interfere with the direct binding of A1 ELC with actin. The efficiency of actin polymerization in the presence of the N-terminal ELC peptides depended on their sequence. Substitution of aspartic acid for neutral asparagine at position 5 of MLCF_pep dramatically enhanced its ability to stimulate S1-induced polymerization and enabled it to initiate polymerization of G-actin in the absence of S1.ConclusionsThese and other results presented in this work suggest that the modulation of myosin motor activity by N-terminal ELC peptides is exerted through a change in actin filament conformation rather than through blocking the A1 ELC-actin interaction.General significanceThe results imply the possibility of enhancing therapeutic effects of these peptides by modifications of their sequence.     

A Novel Family of Unconventional Actins in Volvocalean Algae

The unicellular green alga Chlamydomonas reinhardtii has two actin genes, one encoding a conventional actin (90% amino acid identity with mammalian actin), the other a highly divergent actin (64% identity) named novel actin-like protein (NAP). To see whether the presence of conventional and unconventional actins in a single organism is unique to C. reinhardtii, we searched for genomic sequences related to the NAP sequence in several other species of volvocalean algae. Here we show that Chlamydomonas moewusii and Volvox carteri also have, in addition to a conventional actin, an unconventional actin similar to the C. reinhardtii NAP. Analyses of the deduced protein sequences indicated that the NAP homologues form a distinct group derived from conventional actin.     

Mannose,but not glucose or sucrose,disturbs actin cytoskeleton in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> leaves

A dynamic cytoskeleton able to recognize and respond to both abiotic and biotic stimuli is necessary for the proper functioning of a living cell. The cytoskeleton is involved in cell growth and division, maintenance of cell shape, cytoplasmic streaming, and organelle movements. Numerous studies have focused on the relationships between sugar metabolism, sugar signaling, and the cytoskeleton in yeast and animal cells. Data on such connections in plants are scarce. In the present study we investigated the effects of exogenously delivered sugars on the plant actin cytoskeleton. Detached Arabidopsis thaliana leaves were incubated with sugars for 2 days and the cytoskeleton was visualized using fluorescent-labeled phalloidin. Glucose and sucrose did not influence the pattern of the actin cytoskeleton. In contrast, mannose caused the disappearance of filamentous structures and generated actin foci. The symptoms started to be visible after 24 h of the exposure to mannose. The effect did not occur in Nicotiana tabacum mesophyll cells. This insensitivity was probably due to the presence of phosphomannose isomerase in tobacco cells. Mannose is commonly used as a selection marker for the transformation of plants lacking the enzymes responsible for the metabolism of mannose-6-phosphate. Exposure to this hexose has been linked with DNA fragmentation and a release of cytochrome c from mitochondria. Both responses are treated as features of programmed cell death. However, in our experiments no DNA laddering was observed in mannose-treated Arabidopsis leaves.