Raynaud Disease
No-Reflow Phenomenon
Models, Biological
Calculation of a Gap restoration in the membrane skeleton of the red blood cell: possible role for myosin II in local repair. (1/4476)
Human red blood cells contain all of the elements involved in the formation of nonmuscle actomyosin II complexes (V. M. Fowler. 1986. J. Cell. Biochem. 31:1-9; 1996. Curr. Opin. Cell Biol. 8:86-96). No clear function has yet been attributed to these complexes. Using a mathematical model for the structure of the red blood cell spectrin skeleton (M. J. Saxton. 1992. J. Theor. Biol. 155:517-536), we have explored a possible role for myosin II bipolar minifilaments in the restoration of the membrane skeleton, which may be locally damaged by major mechanical or chemical stress. We propose that the establishment of stable links between distant antiparallel actin protofilaments after a local myosin II activation may initiate the repair of the disrupted area. We show that it is possible to define conditions in which the calculated number of myosin II minifilaments bound to actin protofilaments is consistent with the estimated number of myosin II minifilaments present in the red blood cells. A clear restoration effect can be observed when more than 50% of the spectrin polymers of a defined area are disrupted. It corresponds to a significant increase in the spectrin density in the protein free region of the membrane. This may be involved in a more complex repair process of the red blood cell membrane, which includes the vesiculation of the bilayer and the compaction of the disassembled spectrin network. (+info)Free energy landscapes of encounter complexes in protein-protein association. (2/4476)
We report the computer generation of a high-density map of the thermodynamic properties of the diffusion-accessible encounter conformations of four receptor-ligand protein pairs, and use it to study the electrostatic and desolvation components of the free energy of association. Encounter complex conformations are generated by sampling the translational/rotational space of the ligand around the receptor, both at 5-A and zero surface-to-surface separations. We find that partial desolvation is always an important effect, and it becomes dominant for complexes in which one of the reactants is neutral or weakly charged. The interaction provides a slowly varying attractive force over a small but significant region of the molecular surface. In complexes with no strong charge complementarity this region surrounds the binding site, and the orientation of the ligand in the encounter conformation with the lowest desolvation free energy is similar to the one observed in the fully formed complex. Complexes with strong opposite charges exhibit two types of behavior. In the first group, represented by barnase/barstar, electrostatics exerts strong orientational steering toward the binding site, and desolvation provides some added adhesion within the local region of low electrostatic energy. In the second group, represented by the complex of kallikrein and pancreatic trypsin inhibitor, the overall stability results from the rather nonspecific electrostatic attraction, whereas the affinity toward the binding region is determined by desolvation interactions. (+info)Solid-state NMR and hydrogen-deuterium exchange in a bilayer-solubilized peptide: structural and mechanistic implications. (3/4476)
Hydrogen-deuterium exchange has been monitored by solid-state NMR to investigate the structure of gramicidin M in a lipid bilayer and to investigate the mechanisms for polypeptide insertion into a lipid bilayer. Through exchange it is possible to observe 15N-2H dipolar interactions in oriented samples that yield precise structural constraints. In separate experiments the pulse sequence SFAM was used to measure dipolar distances in this structure, showing that the dimer is antiparallel. The combined use of orientational and distance constraints is shown to be a powerful structural approach. By monitoring the hydrogen-deuterium exchange at different stages in the insertion of peptides into a bilayer environment it is shown that dimeric gramicidin is inserted into the bilayer intact, i.e., without separating into monomer units. The exchange mechanism is investigated for various sites and support for a relayed imidic acid mechanism is presented. Both acid and base catalyzed mechanisms may be operable. The nonexchangeable sites clearly define a central core to which water is inaccessible or hydroxide or hydronium ion is not even momentarily stable. This provides strong evidence that this is a nonconducting state. (+info)Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges. (4/4476)
The results of an all-atom molecular dynamics simulation on a discoidal complex made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and a synthetic alpha-helical 18-mer peptide with an apolipoprotein-like charge distribution are presented. The system consists of 12 acetyl-18A-amide (Ac-18A-NH2) (. J. Biol. Chem. 260:10248-10255) molecules and 20 molecules of POPC in a bilayer, 10 in each leaflet, solvated in a sphere of water for a total of 28,522 atoms. The peptide molecules are oriented with their long axes normal to the bilayer (the "picket fence" orientation). This system is analogous to complexes formed in nascent high-density lipoprotein and to Ac-18A-NH2/phospholipid complexes observed experimentally. The simulation extended over 700 ps, with the last 493 ps used for analysis. The symmetry of this system allows for averaging over different helices to improve sampling, while maintaining explicit all-atom representation of all peptides. The complex is stable on the simulated time scale. Several possible salt bridges between and within helices were studied. A few salt bridge formations and disruptions were observed. Salt bridges provide specificity in interhelical interactions. (+info)Molecular dynamics study of substance P peptides in a biphasic membrane mimic. (5/4476)
Two neuropeptides, substance P (SP) and SP-tyrosine-8 (SP-Y8), have been studied by molecular dynamics (MD) simulation in a TIP3P water/CCl4 biphasic solvent system as a mimic for the water-membrane system. Initially, distance restraints derived from NMR nuclear Overhauser enhancements (NOE) were incorporated in the restrained MD (RMD) in the equilibration stage of the simulation. The starting orientation/position of the peptides for the MD simulation was either parallel to the water/CCl4 interface or in a perpendicular/insertion mode. In both cases the peptides equilibrated and adopted a near-parallel orientation within approximately 250 ps. After equilibration, the conformation and orientation of the peptides, the solvation of both the backbone and the side chain of the residues, hydrogen bonding, and the dynamics of the peptides were analyzed from trajectories obtained in the RMD or the subsequent free MD (where the NOE restraints were removed). These analyses showed that the peptide backbone of nearly all residues are either solvated by water or are hydrogen-bonded. This is seen to be an important factor against the insertion mode of interaction. Most of the interactions with the hydrophobic phase come from the hydrophobic interactions of the side chains of Pro-4, Phe-7, Phe-8, Leu-10, and Met-11 for SP, and Phe-7, Leu-10, Met-11 and, to a lesser extent, Tyr-8 in SP-Y8. Concerted conformational transitions took place in the time frame of hundreds of picoseconds. The concertedness of the transition was due to the tendency of the peptide to maintain the necessary secondary structure to position the peptide properly with respect to the water/CCl4 interface. (+info)Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle. (6/4476)
Two neuropeptides, substance P (SP) and SP-tyrosine-8 (SP-Y8), have been studied by molecular dynamics (MD) simulation in an explicit sodium dodecylsulfate (SDS) micelle. Initially, distance restraints derived from NMR nuclear Overhauser enhancements (NOE) were incorporated in the restrained MD (RMD) during the equilibration stage of the simulation. It was shown that when SP-Y8 was initially placed in an insertion (perpendicular) configuration, the peptide equilibrated to a surface-bound (parallel) configuration in approximately 450 ps. After equilibration, the conformation and orientation of the peptides, the solvation of both the backbone and the side chain of the residues, hydrogen bonding, and the dynamics of the peptides were analyzed from trajectories obtained from the RMD or the subsequent free MD (where the NOE restraints were removed). These analyses showed that the peptide backbones of all residues are either solvated by water or are hydrogen-bonded. This is seen to be an important factor against the insertion mode of interaction. Most of the interactions come from the hydrophobic interaction between the side chains of Lys-3, Pro-4, Phe-7, Phe-8, Leu-10, and Met-11 for SP, from Lys-3, Phe-7, Leu-10, and Met-11 in SP-Y8, and the micellar interior. Significant interactions, electrostatic and hydrogen bonding, between the N-terminal residues, Arg-Pro-Lys, and the micellar headgroups were observed. These latter interactions served to affect both the structure and, especially, the flexibility, of the N-terminus. The results from simulation of the same peptides in a water/CCl4 biphasic cell were compared with the results of the present study, and the validity of using the biphasic system as an approximation for peptide-micelle or peptide-bilayer systems is discussed. (+info)Charge pairing of headgroups in phosphatidylcholine membranes: A molecular dynamics simulation study. (7/4476)
Molecular dynamics simulation of the hydrated dimyristoylphosphatidylcholine (DMPC) bilayer membrane in the liquid-crystalline phase was carried out for 5 ns to study the interaction among DMPC headgroups in the membrane/water interface region. The phosphatidylcholine headgroup contains a positively charged choline group and negatively charged phosphate and carbonyl groups, although it is a neutral molecule as a whole. Our previous study (Pasenkiewicz-Gierula, M., Y. Takaoka, H. Miyagawa, K. Kitamura, and A. Kusumi. 1997. J. Phys. Chem. 101:3677-3691) showed the formation of water cross-bridges between negatively charged groups in which a water molecule is simultaneously hydrogen bonded to two DMPC molecules. Water bridges link 76% of DMPC molecules in the membrane. In the present study we show that relatively stable charge associations (charge pairs) are formed between the positively and negatively charged groups of two DMPC molecules. Charge pairs link 93% of DMPC molecules in the membrane. Water bridges and charge pairs together form an extended network of interactions among DMPC headgroups linking 98% of all membrane phospholipids. The average lifetimes of DMPC-DMPC associations via charge pairs, water bridges and both, are at least 730, 1400, and over 1500 ps, respectively. However, these associations are dynamic states and they break and re-form several times during their lifetime. (+info)Pathways of electron transfer in Escherichia coli DNA photolyase: Trp306 to FADH. (8/4476)
We describe the results of a series of theoretical calculations of electron transfer pathways between Trp306 and *FADH. in the Escherichia coli DNA photolyase molecule, using the method of interatomic tunneling currents. It is found that there are two conformationally orthogonal tryptophans, Trp359 and Trp382, between donor and acceptor that play a crucial role in the pathways of the electron transfer process. The pathways depend vitally on the aromaticity of tryptophans and the flavin molecule. The results of this calculation suggest that the major pathway of the electron transfer is due to a set of overlapping orthogonal pi-rings, which starts from the donor Trp306, runs through Trp359 and Trp382, and finally reaches the flavin group of the acceptor complex, FADH. (+info)Biophysical phenomena refer to the observable events and processes that occur in living organisms, which can be explained and studied using the principles and methods of physics. These phenomena can include a wide range of biological processes at various levels of organization, from molecular interactions to whole-organism behaviors. Examples of biophysical phenomena include the mechanics of muscle contraction, the electrical activity of neurons, the transport of molecules across cell membranes, and the optical properties of biological tissues. By applying physical theories and techniques to the study of living systems, biophysicists seek to better understand the fundamental principles that govern life and to develop new approaches for diagnosing and treating diseases.
Raynaud's disease, also known as Raynaud's phenomenon or syndrome, is a condition that affects the blood vessels, particularly in the fingers and toes. It is characterized by episodes of vasospasm (constriction) of the small digital arteries and arterioles, which can be triggered by cold temperatures or emotional stress. This results in reduced blood flow to the affected areas, causing them to become pale or white and then cyanotic (blue) due to the accumulation of deoxygenated blood. As the episode resolves, the affected areas may turn red as blood flow returns, sometimes accompanied by pain, numbness, or tingling sensations.
Raynaud's disease can be primary, meaning it occurs without an underlying medical condition, or secondary, which is associated with connective tissue disorders, autoimmune diseases, or other health issues such as carpal tunnel syndrome, vibration tool usage, or smoking. Primary Raynaud's is more common and tends to be less severe than secondary Raynaud's.
Treatment for Raynaud's disease typically involves avoiding triggers, keeping the body warm, and using medications to help dilate blood vessels and improve circulation. In some cases, lifestyle modifications and smoking cessation may also be recommended to manage symptoms and prevent progression of the condition.
The "no-reflow" phenomenon is a term used in the medical field, particularly in interventional cardiology and neurology. It refers to the inability to restore blood flow to an organ or tissue despite successful removal of the obstruction in the blood vessel that supplies it. This can occur during procedures such as angioplasty and stenting, where the opening of a narrowed or blocked artery is attempted.
The no-reflow phenomenon is thought to be caused by several factors, including damage to the blood vessel walls, formation of microthrombi (small blood clots), and spasm of the blood vessels. This can lead to further tissue damage and poor clinical outcomes, such as reduced organ function or even death of the tissue in extreme cases.
In the context of cardiology, the no-reflow phenomenon is often seen during percutaneous coronary intervention (PCI) procedures, where the goal is to open up a blocked artery in the heart (coronary artery) to improve blood flow to the heart muscle. Despite successful restoration of blood flow through the use of balloons and stents, some areas of the heart muscle may not receive adequate blood flow due to the no-reflow phenomenon.
In neurology, the no-reflow phenomenon can occur during procedures aimed at restoring blood flow to the brain, such as mechanical thrombectomy for acute ischemic stroke. The presence of the no-reflow phenomenon in this context has been associated with worse clinical outcomes and increased risk of disability or death.
In the field of medicine, "time factors" refer to the duration of symptoms or time elapsed since the onset of a medical condition, which can have significant implications for diagnosis and treatment. Understanding time factors is crucial in determining the progression of a disease, evaluating the effectiveness of treatments, and making critical decisions regarding patient care.
For example, in stroke management, "time is brain," meaning that rapid intervention within a specific time frame (usually within 4.5 hours) is essential to administering tissue plasminogen activator (tPA), a clot-busting drug that can minimize brain damage and improve patient outcomes. Similarly, in trauma care, the "golden hour" concept emphasizes the importance of providing definitive care within the first 60 minutes after injury to increase survival rates and reduce morbidity.
Time factors also play a role in monitoring the progression of chronic conditions like diabetes or heart disease, where regular follow-ups and assessments help determine appropriate treatment adjustments and prevent complications. In infectious diseases, time factors are crucial for initiating antibiotic therapy and identifying potential outbreaks to control their spread.
Overall, "time factors" encompass the significance of recognizing and acting promptly in various medical scenarios to optimize patient outcomes and provide effective care.
Biological models, also known as physiological models or organismal models, are simplified representations of biological systems, processes, or mechanisms that are used to understand and explain the underlying principles and relationships. These models can be theoretical (conceptual or mathematical) or physical (such as anatomical models, cell cultures, or animal models). They are widely used in biomedical research to study various phenomena, including disease pathophysiology, drug action, and therapeutic interventions.
Examples of biological models include:
1. Mathematical models: These use mathematical equations and formulas to describe complex biological systems or processes, such as population dynamics, metabolic pathways, or gene regulation networks. They can help predict the behavior of these systems under different conditions and test hypotheses about their underlying mechanisms.
2. Cell cultures: These are collections of cells grown in a controlled environment, typically in a laboratory dish or flask. They can be used to study cellular processes, such as signal transduction, gene expression, or metabolism, and to test the effects of drugs or other treatments on these processes.
3. Animal models: These are living organisms, usually vertebrates like mice, rats, or non-human primates, that are used to study various aspects of human biology and disease. They can provide valuable insights into the pathophysiology of diseases, the mechanisms of drug action, and the safety and efficacy of new therapies.
4. Anatomical models: These are physical representations of biological structures or systems, such as plastic models of organs or tissues, that can be used for educational purposes or to plan surgical procedures. They can also serve as a basis for developing more sophisticated models, such as computer simulations or 3D-printed replicas.
Overall, biological models play a crucial role in advancing our understanding of biology and medicine, helping to identify new targets for therapeutic intervention, develop novel drugs and treatments, and improve human health.
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Mathematical Methods and Modeling of Biophysical Phenomena - 2011 | IMPA - Instituto de Matemática Pura e Aplicada
Biophysical Phenomena - McMaster Experts
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Poor Sleep Quality Is Associated with Dawn Phenomenon and Impaired Circadian Clock Gene Expression in Subjects with Type 2...
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Environmental Studies - The University of Sydney
Processes4
- It is housed in a 1,350 square-foot laboratory at CERC and will be used to study transport phenomena and biophysical processes in river environments. (usgs.gov)
- The dynamic character of the environment influencing the electron transfer processes highlights phenomena such as pathway interference, conformational transfer gating, or the already mentioned transient resonances 20 in which the traditional picture of a static molecular structure must be replaced by a more dynamic one. (nature.com)
- Using the JURECA supercomputer, a team of University of Cologne researchers led by Prof. Dr. Joseph Kambeitz is simulating biophysical processes in the brain in pursuit of better understanding what leads to schizophrenia in patients. (gauss-centre.eu)
- We present a biophysical characterization of the oligomerization and aggregation processes by Interferon alpha-2a (IFNα-2a), a protein drug with antiviral and immunomodulatory properties. (lu.se)
Biophysics3
- The Department of optical and biophysical systems has 45 team members and exists out of 4 laboratories: the Laboratory of Functional Biointerfaces, the Laboratory of Biophysics, the Laboratory of Pulsed Laser Deposition of Thin Films and the Laboratory of Oxides. (fzu.cz)
- The Laboratory of Biophysics is aiming to create a unique interdisciplinary biophysical platform for complex research and cooperation across physics, chemistry, biology, and medicine, serving at the same time as an excellent research centre for education of students. (fzu.cz)
- Appropriate for graduate students and researchers in biophysics, physics, engineering, biology, and neuroscience, The Molecular Switch presents a unified, quantitative model for describing biological signaling phenomena. (booksamillion.com)
Physical Phenomena1
- This specialisation incorporates both social and bio-physical phenomena within their regulatory and policy frameworks, and is therefore inherently multi-disciplinary. (edu.au)
Chemistry3
- Deepened knowledge on the biophysical chemistry of proteins with emphasis on properties rather than methods. (lu.se)
- In 2008, she was appointed as a Lecturer in Biophysical Chemistry at the Department of Chemistry of the University of Sheffield. (royalsociety.org)
- Biophysical Chemistry. (lu.se)
Understanding of biological phenomena2
- Studying these interactions at the single-molecule level contributes significantly to our understanding of biological phenomena. (biophysics.org)
- The Biophysical Society of Japan is to advance collaboration of researchers from different disciplines by providing a place for exchanging knowledge, methods and techniques and is to promote biological sciences for further understanding of biological phenomena. (biophys.jp)
Proteins1
- They are accumulations of proteins and often also nucleic acids which display particular biophysical properties. (unibas.ch)
Mechanisms3
- Thus, we believe poor sleep quality is one of the core mechanisms in dawn phenomenon. (hindawi.com)
- A significant volume of research performed over an ample amount of time has clarified the biophysical mechanisms through which the inner ear is able to encode sound stimulation into neural signals that are subsequently processed in the auditory brainstem and cerebral cortex. (dailynexus.com)
- The 2023 Ruth Patrick Award will be presented to Dr. Dongyan Liu, for discovering that the Yellow Sea green tide phenomenon initiated with intensive coastal aquaculture, for her research on the biophysical mechanisms and physiological attributes of the algae that explain the extraordinary growth and spread of the blooms, and for her work on mitigation of this significant environmental problem. (aslo.org)
Nonlinear1
- Rhodes, 1999 ), making summation in dendritic trees a highly nonlinear phenomenon the properties of which are just beginning to be unraveled. (jneurosci.org)
Simulations1
- This democratizes the building of large-scale, accurate simulations of physical and biophysical phenomena," such as biological and climate models. (technical.ly)
Scientists3
- This is part of a series of workshops organized by IMPA aiming at bringing together a multidisciplinary group of scientists to study problems in the biophysical sciences upon which mathematics may have an impact. (impa.br)
- A group of scientists at UC Santa Barbara's Kavli Institute for Theoretical Physics (KITP) have come together to investigate the science behind this phenomenon. (dailynexus.com)
- I looked as hard as I could and I could not find any trace of medical scientists worrying about such a phenomenon a priori. (lemire.me)
Properties1
- E. coli production of a multi-disulfide bonded SARS-CoV-2 Omicron BA.5 RBD exhibiting native-like biochemical and biophysical properties' by Rawiwan Wongnak, Subbaian Brindha, Takahiro Yoshizue, Sawaros Onchaiya, Kenji Mizutani, Yutaka Kuroda is published in BPPB as the J-STAGE Advance Publication. (biophys.jp)
Potentially1
- Many basic biophysical questions regarding this potentially important phenomenon have not yet been addressed. (jneurosci.org)
Journal1
- Journal of Research in Psi Phenomena, 1 , 8 43. (bvsalud.org)
Researchers1
- Today, researchers worldwide are studying this phenomenon. (unibas.ch)
Research2
- The Department of optical and biophysical systems conducts cutting edge research in the areas of innovative coating materials, biomedical applications and advanced optical techniques. (fzu.cz)
- The Laboratory of Oxides shares this research area, and also focuses on the creation of novel or improved response functions based on composition-dependent and epitaxy-controlled nanoscale phenomena. (fzu.cz)
Protein1
- Aggregation is a common phenomenon in the field of protein therapeutics and can lead to function loss or immunogenic patient responses. (lu.se)
Society1
- I wasn't really sure what to expect when I was getting ready to come to the Annual Biophysical Society Meeting. (biophysics.org)
Models1
- Also biophysical models presented general basics for this phenomenon. (wikipedia.org)
Study1
- The increased level of automation, in conjunction with advanced optical techniques, makes the new ForceRobot 400 an outstanding tool for the study of biophysical phenomena at the single-molecule scale," said Professor Yi Cao, Department of Physics, Nanjing University, China. (przoom.com)
Mechanism3
- The mechanism of dawn phenomenon still remains unclear. (hindawi.com)
- Some endogenous hormones, especially growth hormone, cortisol, and glucagon, also take part in the pathophysiological mechanism of dawn phenomenon [ 4 , 5 ]. (hindawi.com)
- A fat embolism phenomenon with resultant vascular occlusion is another proposed mechanism. (medscape.com)
Model2
- Accordingly, the phenomena observed in vitro could be reproduced in purely deterministic biophysical model neurons. (yale.edu)
- I will present a biophysical model which explains genome-wide codon frequencies observed across 20 organisms. (rutgers.edu)
Significantly3
- The levels of HbA1c and fasting glucose and the magnitude of dawn phenomenon were significantly higher in the diabetes group with poor sleep quality than that with good sleep quality. (hindawi.com)
- Poor sleep quality was significantly correlated with magnitude of dawn phenomenon. (hindawi.com)
- Multiple linear regression showed that sleep quality and PER1 were significantly independently correlated with dawn phenomenon. (hindawi.com)
Perspective2
- The Molecular Switch articulates a biophysical perspective on signaling, showing how allostery--a powerful explanation of how molecules function across all biological domains--can be reformulated using equilibrium statistical mechanics, applied to diverse biological systems exhibiting switching behaviors, and successfully unify seemingly unrelated phenomena.Rob Phillips weaves together allostery and statistical mechanics via a series of biological vignettes, each of which showcases an important biological question and accompanying physical analysis. (booksamillion.com)
- The Molecular Switch articulates a biophysical perspective on signaling, showing how allostery--a powerful explanation of how molecules function across all biological domains--can be reformulated using equilibrium statistical mechanics, applied to diverse biological systems exhibiting switching behaviors, and successfully unify seemingly unrelated phenomena. (booksamillion.com)
Term1
- The term "dawn phenomenon" was first introduced by Schmidt et al. (hindawi.com)
Studies1
- Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu): synthesis and biophysical studies of Gly-Pro-Nleu sequences by circular dichroism, ultraviolet absorbance, and optical rotation. (mcmaster.ca)
Agents1
- Along with biophysical modalities, agents that have been used for nonoperative management include bisphosphonates, anticoagulants, vasodilators, and statins. (medscape.com)
Level1
- published that the approximate impact of the dawn phenomenon on HbA1c level was 0.4% and the impact for averaged 24 h mean glucose concentrations was 12.4 mg/dL [ 3 ]. (hindawi.com)
High1
- Dawn phenomenon mostly affects children and youth with type 1 diabetes, although it is not rare in subjects with type 2 diabetes (as high as 40%, reported by Monnier et al. (hindawi.com)
Similar2
- We have all observed a similar phenomenon in everyday life. (unibas.ch)
- This transient near-degeneracy enables coherent charge transfer with signatures similar to tunneling, possibly accelerating biophysical reactions. (nature.com)
Scale1
- Her work has been critical to solving the origin of the Yellow Sea green-tides, the world's largest harmful algal blooms that have been a recurrent environmental phenomenon of enormous scale and severity since the first occurrence in 2008. (aslo.org)
Approach1
- Overall, our approach offers a unified biophysical and population genetics framework for understanding codon bias. (rutgers.edu)
Worldwide1
- Her publications on the green tide phenomena have received worldwide attention and have guided successful government controls. (aslo.org)