Propagation of Turing patterns in a plankton model

The paper is devoted to a reaction–diffusion system of equations describing phytoplankton and zooplankton distributions. Linear stability analysis of the model is carried out. Turing and Hopf stability boundaries are found. Emergence of two-dimensional spatial structures is illustrated by numerical simulations. Travelling waves between various stationary solutions are investigated. Transitions between homogeneous in space stationary solutions and Turing structures are studied.     

Formation of banded vegetation patterns resulted from interactions between sediment deposition and vegetation growth

This research investigates the formation of banded vegetation patterns on hillslopes affected by interactions between sediment deposition and vegetation growth. The following two perspectives in the formation of these patterns are taken into consideration: (a) increased sediment deposition from plant interception, and (b) reduced plant biomass caused by sediment accumulation. A spatial model is proposed to describe how the interactions between sediment deposition and vegetation growth promote self-organization of banded vegetation patterns. Based on theoretical and numerical analyses of the proposed spatial model, vegetation bands can result from a Turing instability mechanism. The banded vegetation patterns obtained in this research resemble patterns reported in the literature. Moreover, measured by sediment dynamics, the variation of hillslope landform can be described. The model predicts how treads on hillslopes evolve with the banded patterns. Thus, we provide a quantitative interpretation for coevolution of vegetation patterns and landforms under effects of sediment redistribution.     

Self‐organized partitioning of dynamically localized proteins in bacterial cell division

How cells manage to get equal distribution of their structures and molecules at cell division is a crucial issue in biology. In principle, a feedback mechanism could always ensure equality by measuring and correcting the distribution in the progeny. However, an elegant alternative could be a mechanism relying on self‐organization, with the interplay between system properties and cell geometry leading to the emergence of equal partitioning. The problem is exemplified by the bacterial Min system that defines the division site by oscillating from pole to pole. Unequal partitioning of Min proteins at division could negatively impact system performance and cell growth because of loss of Min oscillations and imprecise mid‐cell determination. In this study, we combine live cell and computational analyses to show that known properties of the Min system together with the gradual reduction of protein exchange through the constricting septum are sufficient to explain the observed highly precise spontaneous protein partitioning. Our findings reveal a novel and effective mechanism of protein partitioning in dividing cells and emphasize the importance of self‐organization in basic cellular processes.     

The relationship between n-gram patterns and protein secondary structure

An n-gram pattern (NP{n,m}) in a protein sequence is a set of n residues and m wildcards in a window of size n+m. Each window of n+m amino acids is associated with a collection of NP{n,m} patterns based on the combinatorics of n+m objects taken m at a time. NP{n,m} patterns that are shared between sequences reflect evolutionary relationships. Recently the authors developed an alignment-independent protein classification algorithm based on shared NP{4,2} patterns that compared favorably to PSI-BLAST. Theoretically, NP{4,2} patterns should also reflect secondary structure propensity since they contain all possible n-grams for 1 < or = n < or = 4 and a window of 6 residues is wide enough to capture periodicities in the 2 < or = n < or = 5 range. This sparked interest in differentiating the information content in NP{4,2} patterns related to evolution from the content related to local propensity. The probability of alpha-, beta-, and coil components was determined for every NP{4,2} pattern over all the chains in the Protein Data Bank (PDB). An algorithm exclusively based on the Z-values of these distributions was developed, which accurately predicted 71-76% of alpha-helical segments and 62-67% of beta-sheets in rigorous jackknife tests. This provided evidence for the strong correlation between NP{4,2} patterns and secondary structure. By grouping PDB chains into subsets with increasing levels of sequence identity, it was also possible to separate the evolutionary and local propensity contributions to the classification process. The results showed that information derived from evolutionary relationships was more important for beta-sheet prediction than alpha-helix prediction.     

Quantitative analysis of time-series fluorescence microscopy using a spot tracking method: application to Min protein dynamics

The dynamics of MinD protein has been recognized as playing an important role in the accurate positioning of the septum during cell division. In this work, spot tracking technique (STT) was applied to track the motion and quantitatively characterize the dynamic behavior of green fluorescent protein-labeled MinD (GFP-MinD) in an Escherichia coli system. We investigated MinD dynamics on the level of particle ensemble or cluster focusing on the position and motion of the maximum in the spatial distribution of MinD proteins. The main results are twofold: (i) a demonstration of how STT could be an acceptable tool for MinD dynamics studies; and (ii) quantitative findings with parametric and non-parametric analyses. Specifically, experimental data monitored from the dividing E. coli cells (typically 4.98 ± 0.75 μm in length) has demonstrated a fast oscillation of the MinD protein between the two poles, with an average period of 54.6 ± 8.6 s. Observations of the oscillating trajectory and velocity show a trapping or localized behavior of MinD around the polar zone, with average localization velocity of 0.29 ± 0.06 μm/s; and flight switching was observed at the pole-to-pole leading edge, with an average switching velocity of 2.95 ± 0.31 μm/s. Subdiffusive motion of MinD proteins at the polar zone was found and investigated with the dynamic exponent, α of 0.34 ± 0.16. To compare with the Gaussian-based analysis, non-parametric statistical analysis and noise consideration were also performed. Co-first authors     

Fluorescence correlation spectroscopy study of protein transport and dynamic interactions with clustered-charge peptide adsorbents

Ion-exchange chromatography relies on electrostatic interactions between the adsorbent and the adsorbate and is used extensively in protein purification. Conventional ion-exchange chromatography uses ligands that are singly charged and randomly dispersed over the adsorbent, creating a heterogeneous distribution of potential adsorption sites. Clustered-charge ion exchangers exhibit higher affinity, capacity, and selectivity than their dispersed-charge counterparts of the same total charge density. In the present work, we monitored the transport behavior of an anionic protein near clustered-charge adsorbent surfaces using fluorescence correlation spectroscopy. We can resolve protein-free diffusion, hindered diffusion, and association with bare glass, agarose-coated, and agarose-clustered peptide surfaces, demonstrating that this method can be used to understand and ultimately optimize clustered-charge adsorbent and other surface interactions at the molecular scale.     

Relationship between protein structures and disulfide-bonding patterns

We found that that disulfide-bonding patterns can be used to discriminate structure similarity. Our method, based on the hierarchical clustering scheme, is applicable to proteins with two or more disulfide bonds and is able to detect the structural similarities of proteins of low sequence identities (<25%). Our results show the surprisingly close relationship between disulfide-bonding patterns and proteins structures. Our findings should be useful in protein structure modeling.     

Collapse transitions in protein-like lattice polymers: The effect of sequence patterns

The collapse transition of lattice protein-like heteropolymers has been studied by means of the Monte Carlo method. The protein model has been reduced to the α-carbon trace restricted to a high coordination lattice. The sequences of model heteropolymers contain two types of mers: hydrophobic/nonpolar (H) and hydrophilic/polar (P). Interactions of HH and PP pairs were assumed to be negative (weaker attractions of PP pairs) while the contact energy for HP pairs was equal to zero. All sequence-specific short-range interactions have been neglected in the present studies. It has been found that homopolymeric chains undergo a smooth collapse transition to a dense globular state. The globule lacks any signatures of local ordering that could be interpreted as a model of protein secondary structure. Hetero-polymers with the sequences of hydrophilic and hydrophobic residues characteristic for α- and β-type proteins undergo a somewhat sharper (though continuous) collapse transition to a dense globular state with elements of local ordering controlled by the sequence. The helical pattern induces more secondary structure than the β-type pattern. For all examined sequences the level of local ordering was lower than the average secondary structure content of globular proteins. The results are compared with other theoretical work and with known experimental facts. The implications for the reduced modeling of protein systems are briefly discussed. © 1997 John Wiley & Sons, Inc. Biopoly 42: 537–548, 1997     

Self-organization and productivity in semi-arid ecosystems: implications of seasonality in rainfall

Spatial self-organization including striking vegetation patterns observed in arid ecosystems has been studied in models with uniform rainfall. In this paper, we present a fully seasonal rainfall model that produces vegetation patterns found in nature by including the natural adaptation of plants to scarcity of water and the consequent seasonal variation in their growth and metabolic rate. We present results for the mean-field and spatially extended versions of the model. We find that the patterns depend on the duration of the wet season even with fixed total annual precipitation (PPT) showing how seasonality affects spatial self-organization. We observe that the productivity can vary for fixed PPT as a function of the duration thereby providing another source of observed variations. We compute the maximum vegetation cover as function of PPT and find that the behavior is consistent with observations. We comment on the implications for regime shifts due to increased interannual fluctuations caused by climatic changes. Our specific model calculations provide more general conclusions for ecosystems with competition for scarce resources due to seasonal variations in the resource, especially for self-organization and productivity.     

Protein patterns in rotifers: the timing of aging

Single rotifer individuals have been characterized biochemically to obtain a fingerprint of their physiological state using a modified ultrasensitive silver-stain procedure to detect total proteins in polyacrylamide gels. Patterns are completely uniform for young isogenic individuals raised in the same culture, but they start to change when these individuals reach a certain age. This age is close to the mean lifespan and to both the cessation of body growth and reproduction. Variability is greatest among individuals of the same chronological age, thus the rate of aging is different even among individuals having identical genotypes and experiencing the same environment.     

In-cell protein NMR and protein leakage

In-cell nuclear magnetic resonance spectroscopy is a tool for studying proteins under physiologically relevant conditions. In some instances, however, protein signals from leaked protein are observed in the liquid surrounding the cells. Here, we examine the expression of four proteins in Escherichia coli. We describe the controls that should be used for in-cell NMR experiments and show that leakage is likely when the protein being studied exceeds ～20% of the total cellular protein.     

Expression of Escherichia coli Min system in Bacillus subtilis and its effect on cell division

In both rod-shaped Bacillus subtilis and Escherichia coli cells, Min proteins are involved in the regulation of division septa formation. In E. coli , dynamic oscillation of MinCD inhibitory complex and MinE, a topological specificity protein, prevents improper polar septation. However, in B. subtilis no MinE is present and no oscillation of Min proteins can be observed. The function of MinE is substituted by that of an unrelated DivIVA protein, which targets MinCD to division sites and retains them at the cell poles. We inspected cell division when the E. coli Min system was introduced into B. subtilis cells. Expression of these heterologous Min proteins resulted in cell elongation. We demonstrate here that E. coli MinD can partially substitute for the function of its B. subtilis protein counterpart. Moreover, E. coli MinD was observed to have similar helical localization as B. subtilis MinD.     

Historical and conceptual background of self-organization by reactive processes

Order, form, pattern and organization are properties central to much living matter. The physicochemical processes by which an initially homogeneous solution of reacting chemicals or biochemicals might self-organize is hence a question of fundamental biological importance. In most cases, solutions of reacting chemicals in a test-tube do not self-organize. Because of this, for many years, it was not thought possible that reactive processes could result in self-organization. However, progressively over the last hundred years, it has been shown that this is not always the case, and under certain conditions, the combination of reaction with molecular diffusion can lead to macroscopic self-organization. In 'complex' systems comprised of populations of strongly coupled elements, new 'emergent' properties, such as self-organization, arise by way of the dynamics of the system. Self-organizing reaction-diffusion systems form a specific type of complex system. Here, I will give a personal overview of the conceptual and historical background to this approach with an emphasis on biological self-organization.     

Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications

All the protein sequences from SWISS-PROT database were analyzed for occurrence of single amino acid repeats, tandem oligo-peptide repeats, and periodically conserved amino acids. Single amino acid repeats of glutamine, serine, glutamic acid, glycine, and alanine seem to be tolerated to a considerable extent in many proteins. Tandem oligo-peptide repeats of different types with varying levels of conservation were detected in several proteins and found to be conspicuous, particularly in structural and cell surface proteins. It appears that repeated sequence patterns may be a mechanism that provides regular arrays of spatial and functional groups, useful for structural packing or for one to one interactions with target molecules. To facilitate further explorations, a database of Tandem Repeats in Protein Sequences (TRIPS) has been developed and is available at URL: http://www.ncl-india.org/trips.     

Regulation of dynamic polarity switching in bacteria by a Ras‐like G‐protein and its cognate GAP

The rod‐shaped cells of the bacterium Myxococcus xanthus move uni‐directionally and occasionally undergo reversals during which the leading/lagging polarity axis is inverted. Cellular reversals depend on pole‐to‐pole relocation of motility proteins that localize to the cell poles between reversals. We show that MglA is a Ras‐like G‐protein and acts as a nucleotide‐dependent molecular switch to regulate motility and that MglB represents a novel GTPase‐activating protein (GAP) family and is the cognate GAP of MglA. Between reversals, MglA/GTP is restricted to the leading and MglB to the lagging pole defining the leading/lagging polarity axis. For reversals, the Frz chemosensory system induces the relocation of MglA/GTP to the lagging pole causing an inversion of the leading/lagging polarity axis. MglA/GTP stimulates motility by establishing correct polarity of motility proteins between reversals and reversals by inducing their pole‐to‐pole relocation. Thus, the function of Ras‐like G‐proteins and their GAPs in regulating cell polarity is found not only in eukaryotes, but also conserved in bacteria.     

长白山北坡林线岳桦种群空间分布格局

许多自然林线具有的趋同特征之一即乔木树种高生长受限,常演化为矮曲状或类似于灌木的形态(即树种的灌木型)占据高山植被带,因此研究林线树种乔木型与灌木型的结构、功能差异有助于进一步理解林线形成的原因。种群分布格局作为种群相对位置定量化描述的基本特征,可以表征物种对环境适应性选择的结果,反应生态过程的综合作用。利用点格局方法,研究长白山北坡林线岳桦种群各生活史阶段、两种生活型的分布格局,结果表明,长白山北坡林线岳桦树高生长受到限制,1.5—3.0m是一个关键的树高生长阶段;相比于老树、中树,幼苗和灌木型岳桦更为均匀,对空间的异质性选择更弱;林线岳桦发育过程中,存在一个生活型分离的重要阶段。此外,相对于老树,灌木型分布更为均匀,表明低矮、多枝这种相对紧凑的生活型更适宜在过渡带生存,乔木型岳桦和灌木型岳桦可能代表着不同的生存策略。     

New intracellular components of bone morphogenetic protein/Smad signaling cascades

Bone morphogenetic proteins (BMPs) regulate many processes in the embryo, including cell type specification, patterning, apoptosis, and epithelial-mesenchymal interaction. They also act in soft and hard tissues in adult life. Their signals are transduced from the plasma membrane to the nucleus through a limited number of Smad proteins. The list of Smad-interacting proteins is however growing and it is clear that these partners determine the outcome of the signal. We summarize the present status in BMP/Smad signaling, with emphasis on recently identified Smad partners and how these proteins may cooperate in the regulation of the expression of BMP target genes.     

Effects of growth rate on cell extract performance in cell-free protein synthesis

Cell-free protein synthesis is a useful research tool and now stands poised to compete with in vivo expression for commercial production of proteins. However, both the extract preparation and protein synthesis procedures must be scaled up. A key challenge is producing the required amount of biomass that also results in highly active cell-free extracts. In this work, we show that the growth rate of the culture dramatically affects extract performance. Extracts prepared from cultures with a specific growth rate of 0.7/h or higher produced approximately 0.9 mg/mL of chloramphenicol acetyl transferase (CAT) in a batch reaction. In contrast, when the source culture growth rate was 0.3/h, the resulting extract produced only 0.5 mg/mL CAT. Examination of the ribosome content in the extracts revealed that the growth rate of the source cells strongly influenced the final ribosome concentration. Polysome analysis of cell-free protein synthesis reactions indicated that about 22% of the total 70S ribosomes are in polysomes for all extracts regardless of growth rate. Furthermore, the overall specific production from the 70S ribosomes is about 22 CAT proteins per ribosome over the course of the reaction in all cases. It appears that rapid culture growth rates are essential for producing a productive extract. However, growth rate does not seem to influence specific ribosome activity. Rather, the increase in extract productivity is a result of a higher ribosome concentration. These results are important for cell-free technology and also suggest an assay for intrinsic in vivo protein synthesis activity.