Microfluidic synthesis of composite cross‐gradient materials for investigating cell–biomaterial interactions

Combinatorial material synthesis is a powerful approach for creating composite material libraries for the high‐throughput screening of cell–material interactions. Although current combinatorial screening platforms have been tremendously successful in identifying target (termed “hit”) materials from composite material libraries, new material synthesis approaches are needed to further optimize the concentrations and blending ratios of the component materials. Here we employed a microfluidic platform to rapidly synthesize composite materials containing cross‐gradients of gelatin and chitosan for investigating cell–biomaterial interactions. The microfluidic synthesis of the cross‐gradient was optimized experimentally and theoretically to produce quantitatively controllable variations in the concentrations and blending ratios of the two components. The anisotropic chemical compositions of the gelatin/chitosan cross‐gradients were characterized by Fourier transform infrared spectrometry and X‐ray photoelectron spectrometry. The three‐dimensional (3D) porous gelatin/chitosan cross‐gradient materials were shown to regulate the cellular morphology and proliferation of smooth muscle cells (SMCs) in a gradient‐dependent manner. We envision that our microfluidic cross‐gradient platform may accelerate the material development processes involved in a wide range of biomedical applications. Biotechnol. Bioeng. 2011; 108:175–185. © 2010 Wiley Periodicals, Inc.     

Cation–π, amino–π, π–π, and H‐bond interactions stabilize antigen–antibody interfaces

The identification of immunogenic regions on the surface of antigens, which are able to stimulate an immune response, is a major challenge for the design of new vaccines. Computational immunology aims at predicting such regions—in particular B‐cell epitopes—but is far from being reliably applicable on a large scale. To gain understanding into the factors that contribute to the antigen–antibody affinity and specificity, we perform a detailed analysis of the amino acid composition and secondary structure of antigen and antibody surfaces, and of the interactions that stabilize the complexes, in comparison with the composition and interactions observed in other heterodimeric protein interfaces. We make a distinction between linear and conformational B‐cell epitopes, according to whether they consist of successive residues along the polypeptide chain or not. The antigen–antibody interfaces were shown to differ from other protein–protein interfaces by their smaller size, their secondary structure with less helices and more loops, and the interactions that stabilize them: more H‐bond, cation–π, amino–π, and π–π interactions, and less hydrophobic packing; linear and conformational epitopes can clearly be distinguished. Often, chains of successive interactions, called cation/amino–π and π–π chains, are formed. The amino acid composition differs significantly between the interfaces: antigen–antibody interfaces are less aliphatic and more charged, polar and aromatic than other heterodimeric protein interfaces. Moreover, paratopes and epitopes—albeit to a lesser extent—have amino acid compositions that are distinct from general protein surfaces. This specificity holds promise for improving B‐cell epitope prediction. Proteins 2014; 82:1734–1746. © 2014 Wiley Periodicals, Inc.     

Latest developments in experimental and computational approaches to characterize protein–lipid interactions

Understanding the functional roles of all the molecules in cells is an ultimate goal of modern biology. An important facet is to understand the functional contributions from intermolecular interactions, both within a class of molecules (e.g. protein–protein) or between classes (e.g. protein‐DNA). While the technologies for analyzing protein–protein and protein–DNA interactions are well established, the field of protein–lipid interactions is still relatively nascent. Here, we review the current status of the experimental and computational approaches for detecting and analyzing protein–lipid interactions. Experimental technologies fall into two principal categories, namely solution‐based and array‐based methods. Computational methods include large–scale data‐driven analyses and predictions/dynamic simulations based on prior knowledge of experimentally identified interactions. Advances in the experimental technologies have led to improved computational analyses and vice versa, thereby furthering our understanding of protein–lipid interactions and their importance in biological systems.     

Effects of human–livestock–wildlife interactions on habitat in an eastern Kenya rangeland

Human–livestock–wildlife interactions have increased in Kenyan rangelands in recent years, but few attempts have been made to evaluate their impact on the rangeland habitat. This study identified drivers of increased human–livestock–wildlife interactions in the Meru Conservation Area between 1980 and 2000 and their effects on the vegetation community structure. The drivers were habitat fragmentation, decline in pastoral grazing range, loss of wildlife dispersal areas and increase in livestock population density. Agricultural encroachment increased by over 76% in the western zone adjoining Nyambene ranges and the southern Tharaka area, substantially reducing the pastoral grazing range and wildlife dispersal areas. Livestock population increased by 41%, subjecting areas left for pastoral grazing in the northern dispersal area to prolonged heavy grazing that gave woody plant species a competitive edge over herbaceous life‐forms. Consequently, open wooded grassland, which was the dominant vegetation community in 1980, decreased by c. 40% as bushland vegetation increased by 42%. A substantial proportion of agro pastoralists were encountered around Kinna and Rapsu, areas that were predominantly occupied by pastoralists three decades ago, indicating a possible shift in land use in order to spread risks associated with habitat alterations.     

Importance of the interaction protein–protein of the CaM–PDE1A and CaM–MLCK complexes in the development of new anti‐CaM drugs

Protein–protein interactions play central roles in physiological and pathological processes. The bases of the mechanisms of drug action are relevant to the discovery of new therapeutic targets. This work focuses on understanding the interactions in protein–protein–ligands complexes, using proteins calmodulin (CaM), human calcium/calmodulin‐dependent 3′,5′‐cyclic nucleotide phosphodiesterase 1A active human (PDE1A), and myosin light chain kinase (MLCK) and ligands αII–spectrin peptide (αII–spec), and two inhibitors of CaM (chlorpromazine (CPZ) and malbrancheamide (MBC)). The interaction was monitored with a fluorescent biosensor of CaM (hCaM M124C–mBBr). The results showed changes in the affinity of CPZ and MBC depending on the CaM–protein complex under analysis. For the Ca²⁺–CaM, Ca²⁺–CaM–PDE1A, and Ca²⁺–CaM–MLCK complexes, CPZ apparent dissociation constants (K_ds) were 1.11, 0.28, and 0.55 μM, respectively; and for MBC K_ds were 1.43, 1.10, and 0.61 μM, respectively. In competition experiments the addition of calmodulin binding peptide 1 (αII–spec) to Ca²⁺–hCaM M124C–mBBr quenched the fluorescence (K_d = 2.55 ± 1.75 pM) and the later addition of MBC (up to 16 μM) did not affect the fluorescent signal. Instead, the additions of αII–spec to a preformed Ca²⁺–hCaM M124C–mBBr–MBC complex modified the fluorescent signal. However, MBC was able to displace the PDE1A and MLCK from its complex with Ca²⁺–CaM. In addition, docking studies were performed for all complexes with both ligands showing an excellent correlation with experimental data. These experiments may help to explain why in vivo many CaM drugs target prefer only a subset of the Ca²⁺–CaM regulated proteins and adds to the understanding of molecular interactions between protein complexes and small ligands. Copyright © 2013 John Wiley & Sons, Ltd.     

Cross‐talk between the insulin‐like growth factor (IGF) axis and membrane integrins to regulate cell physiology

The biology of cross‐talk between activated growth factor receptors and cell‐surface integrins is an area which has attracted much interest in recent years (Schwartz and Ginsberg, 2002 ). This review discusses the relationship between the insulin‐like growth factor (IGF) axis and cell‐surface integrin receptors in the regulation of various aspects of cell physiology. Key to these interactions are signals transmitted between integrins and the IGF‐I receptor (IGF‐IR) when either or both are bound to their cognate ligands and we will review the current state of knowledge in this area. The IGF axis comprises many molecular components and we will also discuss the potential role of these species in cross‐talk with the integrin receptor. With respect to integrin ligands, we will mainly focus on the well‐characterized interactions of the two extracellular matrix (ECM) glycoproteins fibronectin (FN) and vitronectin (VN) with cell‐surface ligands, and, how this affects activity through the IGF axis. However, we will also highlight the importance of other integrin activation mechanisms and their impact on IGF activity. J. Cell. Physiol. 224: 605–611, 2010. © 2010 Wiley‐Liss, Inc.     

Detection of cellular response to titanium dioxide nanoparticle agglomerates by sensor cells using heat shock protein promoter

Nanotechnology is becoming increasingly important for products used in our daily lives, such as the masses of titanium dioxide nanoparticle agglomerates (TiO₂ NPs) used in the pharmaceutical industry, for cosmetic products, or for pigments. Meanwhile, a serious lack of detailed information concerning the interaction between the nanomaterials and cells limits their biological and medical applications. Sensing technology is very important for understanding these interactions. We have shown that TiO₂ NPs induce heat shock protein 70B' (HSP70B') mRNA [Okuda‐Shimazaki et al., 2010. Int J Mol Sci 11:2383–2392]. In the current work, sensor cells for detection of cellular responses to NPs were prepared by transfecting an HSP70B' promoter–reporter plasmid. First, to find suitable cells for detection, five different mammalian cell lines were chosen as potential sensor cells. The results showed TiO₂ NP response in some cell lines, although different sensor cells had different TiO₂ NP response levels, as heat shock response ability is important for the detection. Then, we studied the TiO₂ NP time‐course response and dose response. The results indicated that our sensor cells can detect TiO₂ NP cellular responses. Our work should aid in understanding the interactions between bio‐nanomaterials and cells. Biotechnol. Bioeng. 2012; 109: 3112–3118. © 2012 Wiley Periodicals, Inc.     

Sperm morphology and the evolution of intracellular sperm–egg interactions

Sperm morphology is incredibly diverse, even among closely related species, yet the coevolution between males and females of fertilization recognition systems is necessary for successful karyogamy (male and female pronuclear fusion). In most species, the entire sperm enters the egg during fertilization so sperm morphological diversity may impact the intracellular sperm–egg interactions necessary for karyogamy. We quantified morphological variation of sperm inside eggs prior to and following karyogamy in several species of Drosophila to understand whether evolution of sperm morphology could influence intracellular sperm–egg interactions (ISEIs). We measured seven parameters that describe ISEIs among species to determine whether these parameters varied both within a species across development and across species at the same developmental stage. We used heterospecific crosses to test the relative role of male origin, female origin, and interaction between the male and female in determining ISEIs. We found that sperm shape changed within a species as development proceeded and, at particular development stages, species varied in some ISEIs. Parental origin had an effect on some ISEIs, with a general trend for a stronger female effect. Overall, our findings identify conserved and variable ISEIs among species and demonstrate the potential to contribute understanding to gamete evolution and development.     

Generation of an EphA4 conditional allele in mice

Ephrins and Eph receptor tyrosine kinases are cell‐surface molecules that serve a multitude of functions in cell–cell communication in development, physiology, and disease. EphA4 is a promiscuous member of the EphA subclass of Eph receptors and can bind to both EphrinAs and EphrinBs. In addition to its well‐established roles in guiding the development of neuronal connectivity, EphA4 has been implicated for a role in synaptic plasticity, vascular formation, axon regeneration, and central nervous system repair following injury. However, the study of its role in the adult stage has been hampered by confounding developmental defects in EphA4 germline mutants. Here, we report the generation and molecular characterization of an EphA4 conditional allele along with a novel null allele with a knockin fluorescent reporter gene (mCFP). The conditional allele will be useful in ascertaining postdevelopmental and/or cell type‐specific function of EphA4 in physiology, injury, and disease. genesis 48:101–105, 2010. © 2009 Wiley‐Liss, Inc.     

Neuronal development in the Drosophila retina

Nervous systems of higher organisms are comprised of a variety of cell types which are interconnected in a precise manner. The molecular mechanisms that lead to the specification of neuronal cell types are not well understood. The compound eye of the fruit fly Drosophila is an attractive experimental system to understand these mechanism. The compound eye is a reiterated neural pattern with several hundred unit structures and is amenable to both classical and molecular genetic methods. During the development of the compound eye cell–cell interactions and positional information play a critical role in the determination of cell fate. Recent genetic and molecular studies have provided important clues regarding the nature of the molecules involved in cellular signalling and neuronal differentiation. © 1993 John Wiley & Sons, Inc.     

The carbon–nutrient balance hypothesis: its rise and fall

The idea that the concentration of secondary metabolites in plant tissues is controlled by the availability of carbon and nitrogen in the environment has been termed the carbon–nutrient balance hypothesis (CNB). This hypothesis has been invoked both for prediction and for post hoc explanation of the results of hundreds of studies. Although it successfully predicts outcomes in some cases, it fails to such an extent that it cannot any longer be considered useful as a predictive tool. As information from studies has accumulated, many attempts have been made to save CNB, but these have been largely unsuccessful and have managed only to limit its utility. The failure of CNB is rooted in assumptions that are now known to be incorrect and it is time to abandon CNB because continued use of the hypothesis is now hindering understanding of plant–consumer interactions. In its place we propose development of theory with a firm evolutionary basis that is mechanistically sophisticated in terms of plant and herbivore physiology and genetics.     

Wnt/β‐catenin signaling during early vertebrate neural development

The vertebrate central nervous system (CNS) is comprised of vast number of distinct cell types arranged in a highly organized manner. This high degree of complexity is achieved by cellular communication, including direct cell‐cell contact, cell‐matrix interactions, and cell‐growth factor signaling. Among the several developmental signals controlling the development of the CNS, Wnt proteins have emerged as particularly critical and, hence, have captivated the attention of many researchers. With Wnts' evolutionarily conserved function as primordial symmetry breaking signals, these proteins and their downstream effects are responsible for simultaneously establishing cellular diversity and tissue organization. With their expansive repertoire of secreted agonists and antagonists, cell surface receptors, signaling cascades and downstream biological effects, Wnts are ideally suited to control the complex processes underlying vertebrate neural development. In this review, we will describe the mechanisms by which Wnts exert their potent effects on cells and tissues and highlight the many roles of Wnt signaling during neural development, starting from the initial induction of the neural plate, the subsequent patterning along the embryonic axes, to the intricately organized structure of the CNS. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1239–1259, 2017     

Anthropogenic increase in carbon dioxide modifies plant–insect interactions

Industrialisation has elevated atmospheric levels of CO₂ from original 280 ppm to current levels at 400 ppm, which is estimated to double by 2050. Although high atmospheric CO₂ levels affect insect interactions with host plants, the impact of global change on plant defences in response to insect attack is not completely understood. Recent studies have made advances in elucidating the mechanisms of the effects of high CO₂ levels in plant–insect interactions. New studies have proposed that gene regulation and phytohormones regulate resource allocation from photosynthesis to plant defences against insects. Biochemical and molecular studies demonstrated that both defensive hormones jasmonic acid (JA) and ethylene (ET) participate in modulating chemical defences against herbivores in plants grown under elevated CO₂ atmosphere rather than changes in C:N ratio. High atmospheric CO₂ levels increase vulnerability to insect damage by down‐regulating both inducive and constitutive chemical defences regulated by JA and ET. However, elevated CO₂ levels increase the JA antagonistic hormone salicylic acid that increases other chemical defences. How plants grown under elevated CO₂ environment allocate primary metabolites from photosynthesis to secondary metabolism would help to understand innate defences and prevent future herbivory in field crops. We present evidence demonstrating that changes in chemical defences in plants grown under elevated CO₂ environment are hormonal regulated and reject the C:N hypothesis. In addition, we discuss current knowledge of the mechanisms that regulate plants defences against insects in elevated CO₂ atmospheres.     

Target cell contact suppresses neurite outgrowth from soma–soma paired Lymnaea neurons

Neurite extension from developing and/or regenerating neurons is terminated on contact with their specific synaptic partner cells. However, a direct relationship between the effects of target cell contact on neurite outgrowth suppression and synapse formation has not yet been demonstrated. To determine whether physical/synaptic contacts affect neurite extension from cultured cells, we utilized soma–soma synapses between the identified Lymnaea neurons. A presynaptic cell (right pedal dorsal 1, RPeD1) was paired either with its postsynaptic partner cells (visceral dorsal 4, VD4, and Visceral dorsal 2, VD2) or with a non‐target cell (visceral dorsal 1, VD1), and the interactions between their neurite outgrowth patterns and synapse formation were examined. Specifically, when cultured in brain conditioned medium (CM, contains growth‐promoting factors), RPeD1, VD4, and VD2 exhibited robust neurite outgrowth within 12–24 h of their isolation. Synapses, similar to those seen in vivo, developed between the neurites of these cells. RPeD1 did not, however, synapse with its non–target cell VD1, despite extensive neuritic overlap between the cells. When placed in a soma–soma configuration (somata juxtaposed against each other), appropriate synapses developed between the somata of RPeD1 and VD4 (inhibitory) and between RPeD1 and VD2 (excitatory). Interestingly, pairing RPeD1 with either of its synaptic partner (VD4 or VD2) resulted in a complete suppression of neurite outgrowth from both pre‐ and postsynaptic neurons, even though the cells were cultured in CM. A single cell in the same dish, however, extended elaborate neurites. Similarly, a postsynaptic cell (VD4) contact suppressed the rate of neurite extension from a previously sprouted RPeD1. This suppression of the presynaptic growth cone motility was also target cell contact specific. The neurite suppression from soma–soma paired cells was transient, and neuronal sprouting began after a delay of 48–72 h. In contrast, when paired with VD1, both RPeD1 and this non‐target cell exhibited robust neurite outgrowth. We demonstrate that this neurite suppression from soma–soma paired cells was target cell contact/synapse specific and Ca²⁺ dependent. Specifically, soma–soma pairing in CM containing either lower external Ca²⁺ concentration (50% of its control level) or Cd²⁺ resulted in robust neurite outgrowth from both cells; however, the incidence of synapse formation between the paired cells was significantly reduced. Taken together, our data show that contact (physical and/or synaptic) between synaptic partners strongly influence neurite outgrowth patterns of both pre‐ and postsynaptic neurons in a time‐dependent and cell‐specific manner. Moreover, our data also suggest that neurite outgrowth and synapse formation are differentially regulated by external Ca²⁺ concentration. © 2000 John Wiley & Sons, Inc. J Neurobiol 42: 357–369, 2000     

Examining post‐translational modification‐mediated protein–protein interactions using a chemical proteomics approach

Post‐translational modifications (PTM) of proteins can control complex and dynamic cellular processes via regulating interactions between key proteins. To understand these regulatory mechanisms, it is critical that we can profile the PTM‐dependent protein–protein interactions. However, identifying these interactions can be very difficult using available approaches, as PTMs can be dynamic and often mediate relatively weak protein–protein interactions. We have recently developed CLASPI (cross‐linking‐assisted and stable isotope labeling in cell culture‐based protein identification), a chemical proteomics approach to examine protein–protein interactions mediated by methylation in human cell lysates. Here, we report three extensions of the CLASPI approach. First, we show that CLASPI can be used to analyze methylation‐dependent protein–protein interactions in lysates of fission yeast, a genetically tractable model organism. For these studies, we examined trimethylated histone H3 lysine‐9 (H3K9Me₃)‐dependent protein–protein interactions. Second, we demonstrate that CLASPI can be used to examine phosphorylation‐dependent protein–protein interactions. In particular, we profile proteins recognizing phosphorylated histone H3 threonine‐3 (H3T3‐Phos), a mitotic histone “mark” appearing exclusively during cell division. Our approach identified survivin, the only known H3T3‐Phos‐binding protein, as well as other proteins, such as MCAK and KIF2A, that are likely to be involved in weak but selective interactions with this histone phosphorylation “mark”. Finally, we demonstrate that the CLASPI approach can be used to study the interplay between histone H3T3‐Phos and trimethylation on the adjacent residue lysine 4 (H3K4Me₃). Together, our findings indicate the CLASPI approach can be broadly applied to profile protein–protein interactions mediated by PTMs.     

ScRALF3, a secreted RALF‐like peptide involved in cell–cell communication between the sporophyte and the female gametophyte in a solanaceous species

Small peptides have been shown to regulate numerous aspects of plant development through cell–cell communication. These signaling events are particularly important during reproduction, regulating gamete development and embryogenesis. Rapid alkalinization factor (RALF)‐like genes, a large gene family that encodes secreted peptides, have specific or ubiquitous expression patterns. Previously, five RALF‐like genes with potential involvement during reproduction were isolated from Solanum chacoense. Here, we show that ScRALF3 is an important peptide regulator of female gametophyte development. Its expression, which is auxin‐inducible, is strictly regulated before and after fertilization. Down‐regulation of ScRALF3 expression by RNA interference leads to the production of smaller fruits that produce fewer seeds, due to improper development of the embryo sacs. Defects include loss of embryo sac nuclei polarization, as well as an increase in asynchronous division, accounting for cellular dysfunctions and premature embryo sac development arrest during megagametogenesis. ScRALF3 is expressed in the sporophytic tissue surrounding the embryo sac, the integument and the nucellus, as revealed by in situ hybridization and GUS staining. As expected for a secreted peptide, fluorescence from an ScRALF3–GFP fusion construct is detected throughout the secretory pathway. Therefore, the ScRALF3 secreted peptide may be directly involved in the regulation of multiple aspects of cell–cell communication between the female gametophyte and its surrounding sporophytic tissue during ovule development.