Inhibitory effects of novel integrin-targeting peptides on angiogenesis activity in HUVEC cells in vitro

Integrins are critically involved in many tumour-promoting activities. The development of inhibitors against integrins may suppress tumour growth by inhibiting tumour angiogenic signalling. In this study, we investigated the effects of two novel peptides containing the integrin binding arginine-glycine-aspartic acid-motif on inhibiting diverse cell behaviours, including cell adhesion, motility, invasion, tube formation and cell cytoskeleton. Cell adhesion and motility assays demonstrated that cyclopeptides c-Gly and c-Lys might inhibit the adhesive and motile activity at the concentration of 25 μM. There was no significant effect on cell invasion, indicating the importance of extracellular matrix degradation in modulating the anti-invasive effect of human umbilical vein endothelial cells (HUVECs). More importantly, the tubular network formation of HUVECs was significantly inhibited by cyclopeptide c-Lys besides causing a remarkable inhibition of cytoskeletal organization, disrupting the focal adhesion and actin stress fibres formation. In conclusion, this study results indicated that the novel peptide c-Lys has the ability to inhibit diverse cell behaviours of HUVECs, and the effects may be mediated at different levels of the tumour growth. Therefore, c-Lys is perhaps proposed to be a potent anti-angiogenic drug candidate.     

Identifying roles for neurotransmission in circuit assembly: insights gained from multiple model systems and experimental approaches

In the adult nervous system, chemical neurotransmission between neurons is essential for information processing. However, neurotransmission is also important for patterning circuits during development, but its precise roles have yet to be identified, and some remain highly debated. Here, we highlight viewpoints that have come to be widely accepted or still challenged. We discuss how distinct techniques and model systems employed to probe the developmental role of neurotransmission may reconcile disparate ideas. We underscore how the effects of perturbing neurotransmission during development vary with model systems, the stage of development when transmission is altered, the nature of the perturbation, and how connectivity is assessed. Based on findings in circuits with connectivity arranged in layers, we raise the possibility that there exist constraints in neuronal network design that limit the role of neurotransmission. We propose that activity-dependent mechanisms are effective in refining connectivity patterns only when inputs from different cells are close enough, spatially, to influence each other's outcome.     

Historical effect in the territoriality of ayu fish

Ayu fish form algae-feeding territories in a river during a non-breeding (growing) season. We build a cost-benefit theory to describe the breakdown and formation of territory. In the early stage of a growing season, all fish hold territories at low densities. Once all territory sites are occupied, excess fish become floaters. When fish density further increases, a phase transition occurs: all the territories suddenly break down and fish form a school. In contrast, when the fish density is decreased, territories are suddenly formed from the school. Both theory and experiments demonstrate that ayu should exhibit a historical effect: the breakdown and formation processes of territory are largely different. In particular, the theory in formation process predicts a specific fish behavior: an “attempted territory holder” that tries to have a small territory emerges just before the formation of territory.     

Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences

Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of −0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm.     

Building stable chains with motile agents: Insights into the morphology of enteric neural crest cell migration

A defining characteristic of the normal development of the enteric nervous system (ENS) is the existence of an enteric neural crest (ENC) cell colonization wave, where the ENC cells form stable chains often associated with axons and near the vascular network. However, within this evolving neural network, the individual ENC cell elements constantly move, change direction and appear to act independently of neighbors. Three possible hypotheses are investigated. The simplest of these postulates that the ENS follows the vascular network as a template. We present evidence which does not support this hypothesis. Two viable alternatives are either that (i) the axons muster the ENC cells, providing the pattern for the chain migration or (ii) ENC cells form chains and the axons follow these paths. These two hypotheses are explored by developing a stochastic cellular automata model, where ENC agents follow simple rules, which reflect the underlying biology of movement, proliferation and differentiation. By simulating ENC precursors and the associated neurons and axons, two models with different fundamental mechanisms are developed. From local rules, a mesoscale network pattern with lacunae emerges, which can be analyzed quantitatively. Simulation and analysis establishes the parameters that affect the morphology of the resulting network. This investigation into the axon/ENC and ENC/ENC interplay suggests possible explanations for observations in mouse and avian embryos in normal and abnormal ENS development, as well as further experimentation.     

Specific binding of activated Vip3Aa10 to Helicoverpa armigera brush border membrane vesicles results in pore formation

Helicoverpa armigera is one of the most harmful pests in China. Although it had been successfully controlled by Cry1A toxins, some H. armigera populations are building up resistance to Cry1A toxins in the laboratory. Vip3A, secreted by Bacillus thuringiensis, is another potential toxin against H. armigera. Previous reports showed that activated Vip3A performs its function by inserting into the midgut brush border membrane vesicles (BBMV) of susceptible insects. To further investigate the binding of Vip3A to BBMV of H. armigera, the full-length Vip3Aa10 toxin expressed in Escherichia coli was digested by trypsin or midgut juice extract, respectively. Among the fragments of digested Vip3Aa10, only a 62 kDa fragment (Vip3Aa10-T) exhibited binding to BBMV of H. armigera and has insecticidal activity. Moreover, this interaction was specific and was not affected by the presence of Cry1Ab toxin. Binding of Vip3Aa10-T to BBMV resulted in the formation of an ion channel. Unlike Cry1A toxins, Vip3Aa10-T was just slightly associated with lipid rafts of BBMV. These data suggest that although activated Vip3Aa10 specifically interacts with BBMV of H. armigera and forms an ion channel, the mode of action of it may be different from that of Cry1A toxins.     

Energetics of metamorphosis in Drosophila melanogaster

We measured the energetic cost of metamorphosis in the fruitfly, Drosophila melanogaster. Metabolic rates decreased rapidly in the first 24 h and remained low until shortly before eclosion, when the rates increased rapidly, thus creating a U-shaped metabolic curve. The primary fuel used during metamorphosis was lipid, which accounted for >80% of total metabolism. The total energy consumed during metamorphosis was lowest at 25 °C, compared to 18 and 29 °C, due to differences in metabolic rates and the length of pupal development. Temperature differentially affected metabolic rates during different stages of metamorphosis. Prepupal and late pupal stages exhibited typical increases in metabolic rate at high temperatures, whereas metabolic rates were independent of temperature during the first 2/3 of pupal development.We tested two hypotheses for the underlying cause of the U-shaped metabolic curve. The first hypothesis was that pupae become oxygen restricted as a result of remodeling of the larval tracheal system. We tested this hypothesis by exposing pupae to hypoxic and hyperoxic atmospheres, and by measuring lactic acid production during normoxic development. No evidence for oxygen limitation was observed. We also tested the hypothesis that the U-shaped metabolic curve follows changes in metabolically active tissue, such that the early decrease in metabolic rates reflects the histolysis of larval tissues, and the later increase in metabolic rates is associated with organogenesis and terminal differentiation of adult tissues. We assayed the activity of a mitochondrial indicator enzyme, citrate synthase, and correlated it with tissue-specific developmental events during metamorphosis. Citrate synthase activity exhibited a U-shaped curve, suggesting that the pattern of metabolic activity is related to changes in the amount of potentially active aerobic tissue.     

Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation

To understand the nature and function of bacterial biofilm and the process of its formation, we have performed systematic screening of a complete set of Escherichia coli genes/open reading frames (ORFs) to identify those that affect biofilm development upon over-expression. In contrast to the biofilm of strain AG1 used as a control, some of the genes/ORFs when over-expressed led to the formation of an abnormal biofilm such as thin, mat-like, filamentous or one easily detaching from various surfaces. Disruptants of selected genes were constructed in order to clarify their roles in the different stages of biofilm formation. Our results suggest that diverse metabolic pathways contribute to the development of biofilm.     

Recent identification of an ERK signal gradient governing planarian regeneration

Planarians have strong regenerative abilities derived from their adult pluripotent stem cell (neoblast) system. However, the molecular mechanisms involved in planarian regeneration have long remained a mystery. In particular, no anterior-specifying factor(s) could be found, although Wnt family proteins had been successfully identified as posterior-specifying factors during planarian regeneration (Gurley et al., 2008, Petersen and Reddien, 2008). A recent textbook of developmental biology therefore proposes a Wnt antagonist as a putative anterior factor (Gilbert, 2013). That is, planarian regeneration was supposed to be explained by a single decreasing gradient of the β-catenin signal from tail to head. However, recently we succeeded in demonstrating that in fact the extracellular-signal regulated kinases (ERK) form a decreasing gradient from head to tail to direct the reorganization of planarian body regionality after amputation (Umesono et al., 2013).     

Bursts of CO2 released during freezing offer a new perspective on avoidance of winter embolism in trees

MethodsCO₂ efflux measurements were conducted during freezing experiments for saplings of three Scots pine (Pinus sylvestris) and three Norway spruce (Picea abies) trees under laboratory conditions, and the magnitudes of the freezing-related bursts of CO₂ released from the stems were analysed using a previously published mechanistic model of CO₂ production, storage, diffusion and efflux from a tree stem. The freezing-related bursts of CO₂ released from a mature Scots pine tree growing in field conditions were also measured and analysed.ConclusionsAll gases dissolved in the xylem sap are not trapped within the ice in the stem during freezing, as has previously been assumed, thus adding a new dimension to the understanding of winter embolism formation. The conduit water volume not only determines the volume of bubbles formed during freezing, but also the efficiency of gas efflux out of the conduit during the freezing process.