Glycan Profiling of Plant Cell Wall Polymers using Microarrays

Plant cell walls are complex matrixes of heterogeneous glycans which play an important role in the physiology and development of plants and provide the raw materials for human societies (e.g. wood, paper, textile and biofuel industries)^1,2. However, understanding the biosynthesis and function of these components remains challenging.Cell wall glycans are chemically and conformationally diverse due to the complexity of their building blocks, the glycosyl residues. These form linkages at multiple positions and differ in ring structure, isomeric or anomeric configuration, and in addition, are substituted with an array of non-sugar residues. Glycan composition varies in different cell and/or tissue types or even sub-domains of a single cell wall³. Furthermore, their composition is also modified during development¹, or in response to environmental cues⁴.In excess of 2,000 genes have Plant cell walls are complex matrixes of heterogeneous glycans been predicted to be involved in cell wall glycan biosynthesis and modification in Arabidopsis⁵. However, relatively few of the biosynthetic genes have been functionally characterized ^4,5. Reverse genetics approaches are difficult because the genes are often differentially expressed, often at low levels, between cell types⁶. Also, mutant studies are often hindered by gene redundancy or compensatory mechanisms to ensure appropriate cell wall function is maintained⁷. Thus novel approaches are needed to rapidly characterise the diverse range of glycan structures and to facilitate functional genomics approaches to understanding cell wall biosynthesis and modification.Monoclonal antibodies (mAbs)^8,9 have emerged as an important tool for determining glycan structure and distribution in plants. These recognise distinct epitopes present within major classes of plant cell wall glycans, including pectins, xyloglucans, xylans, mannans, glucans and arabinogalactans. Recently their use has been extended to large-scale screening experiments to determine the relative abundance of glycans in a broad range of plant and tissue types simultaneously^9,10,11.Here we present a microarray-based glycan screening method called Comprehensive Microarray Polymer Profiling (CoMPP) (Figures 1 & 2)^10,11 that enables multiple samples (100 sec) to be screened using a miniaturised microarray platform with reduced reagent and sample volumes. The spot signals on the microarray can be formally quantified to give semi-quantitative data about glycan epitope occurrence. This approach is well suited to tracking glycan changes in complex biological systems¹² and providing a global overview of cell wall composition particularly when prior knowledge of this is unavailable.     

Native and Introduced Ecosystem Engineers Produce Contrasting Effects on Estuarine Infaunal Communities

Cordgrasses in the genus Spartina are good examples of ecosystem engineers that modify habitat structure in estuaries throughout the world. In San Francisco Bay, California, USA, marshes containing native California cordgrass (Spartina foliosa) are being invaded by a hybrid (S. alterniflora × S. foliosa) formed after introduction of S. alterniflora. This study compared vegetation, sediment structure, and infaunal invertebrates in native and invaded marshes. We hypothesized that differences in the physical structure between S. foliosa and hybrid Spartina would be reflected in differences in density, biomass, diversity, and taxonomic composition of infauna. Hybrid Spartina modifies habitat structure more than S. foliosa by producing taller stems, and greater plant biomass both above- and belowground while occupying a much wider tidal range, thereby transforming open mudflats to a vegetated habitat. In general, S. foliosa areas contained significantly higher densities of benthic infauna than adjacent mudflats, while hybrid Spartina areas never contained greater infaunal densities than mudflats. This is because S. foliosa produces a moderate level of structure that can facilitate benthic invertebrates, whereas hybrid Spartina produces so much structure, particularly belowground, that it actually excludes invertebrates. Therefore, we suggest that these two closely related species both act as ecosystem engineers, but with opposing effects on invertebrate communities.     

Schizophrenia Gene Networks and Pathways and Their Applications for Novel Candidate Gene Selection

Background

Schizophrenia (SZ) is a heritable, complex mental disorder. We have seen limited success in finding causal genes for schizophrenia from numerous conventional studies. Protein interaction network and pathway-based analysis may provide us an alternative and effective approach to investigating the molecular mechanisms of schizophrenia.

Methodology/Principal Findings

We selected a list of schizophrenia candidate genes (SZGenes) using a multi-dimensional evidence-based approach. The global network properties of proteins encoded by these SZGenes were explored in the context of the human protein interactome while local network properties were investigated by comparing SZ-specific and cancer-specific networks that were extracted from the human interactome. Relative to cancer genes, we observed that SZGenes tend to have an intermediate degree and an intermediate efficiency on a perturbation spreading throughout the human interactome. This suggested that schizophrenia might have different pathological mechanisms from cancer even though both are complex diseases. We conducted pathway analysis using Ingenuity System and constructed the first schizophrenia molecular network (SMN) based on protein interaction networks, pathways and literature survey. We identified 24 pathways overrepresented in SZGenes and examined their interactions and crosstalk. We observed that these pathways were related to neurodevelopment, immune system, and retinoic X receptor (RXR). Our examination of SMN revealed that schizophrenia is a dynamic process caused by dysregulation of the multiple pathways. Finally, we applied the network/pathway approach to identify novel candidate genes, some of which could be verified by experiments.

Conclusions/Significance

This study provides the first comprehensive review of the network and pathway characteristics of schizophrenia candidate genes. Our preliminary results suggest that this systems biology approach might prove promising for selection of candidate genes for complex diseases. Our findings have important implications for the molecular mechanisms for schizophrenia and, potentially, other psychiatric disorders.     

Ca2+-triggered simultaneous membrane penetration of the tandem C2-domains of synaptotagmin I

Synaptotagmin I (syt), a transmembrane protein localized to secretory vesicles, functions as a Ca2+ sensor that facilitates SNARE-mediated membrane fusion. The cytoplasmic domain of syt harbors two C2-domains designated C2A and C2B. Upon binding Ca2+, C2A and C2B partially penetrate into membranes that contain anionic phospholipids. However, it is unknown whether these tandem C2-domains engage membranes at the same time, in a sequential manner, or in a mutually exclusive manner. We have used site-directed fluorescent probes to monitor the penetration of syt's C2-domains into phosphatidylserine-harboring lipid bilayers. We report that, in response to Ca2+, C2A and C2B copenetrate into these bilayers with diffusion-limited kinetics. Membrane penetration was more efficient when synthetic rather than natural phospholipids were used to prepare bilayers. The membrane penetration activity of the intact cytoplasmic domain of syt (C2A-C2B) exhibits significant resistance to changes in ionic strength. In contrast, the ability of isolated C2B to bind membranes in response to Ca2+ can be disrupted by subtle changes in ionic strength. Tethering C2B to a mutant version of C2A that does not bind Ca2+ or membranes significantly increases the stability of Ca2+.C2B.membrane complexes, confirming that C2A affects the membrane-binding properties of the adjacent C2B domain.     

Quantitative estimation of pancreatic polypeptide (PP) cells of islet tissue of pancreas in Australian mammals

Pancreases from three male and three female echidnas ( Tachyglossus aculeatus ), possums ( Trichosurus vulpecula ), grey kangaroos ( Macropus fuliginosus ), spinifex hopping mice ( Notomys alexis ) and water rats ( Hydromys chrysogaster ) were studied using a point-intercept method and Weibel graticule (Weibel, Kistler & Scherle, 1966) on sections stained by an immunoperoxidase method for pancreatic polypeptide (PP). PP cells were assessed in the head, neck, body and tail regions. There was a greater percentage proportion of PP cells in the head than in the other regions of echidna, possum and water rat. PP cells were not identified in grey kangaroo and spinifex hopping mouse, although control sections were positive.
These results show some agreement with a previously proposed hypothesis (Bonner-Weir & Weir, 1979) concerning the distribution of cell types in the mammalian endocrine pancreas.     

Sterilization of Regenerated Collagen Sutures with β-Propiolactone

Data are presented to show that β-propiolactone when properly applied is a very effective agent for sterilization of regenerated collagen sutures. The chemical sterilization is accomplished with little or none of the loss in strength encountered with heat sterilization. The finished sterile suture is obtained without any harmful residue that might be detrimental to the patient.     

Earthworm coelomocytes in vitro

Summary Contamination and low viability of earthworm coelomocytes in tissue culture have delayed in vitro studies. Using penicillin, streptomycin, tetracycline and Amphotericin B,Lumbricus terrestis coelomocytes were maintained viable and uncontaminated for 10 days at 15°C in medium L-15 supplemented with 5 to 10% fetal bovine serum. The coelomocytes survived for at least 10 days with 85% viability as assessed by trypan blue exclusion assays and phagocytosis of heat-killed yeast. Studies on the thymidine uptake, however, were negative. With the involvement of coelomocytes in tissue graft rejection, in vitro techniques can now be applied to study their capacity in the immune response. Supported in part by USPHS Research Grant 1 RO 1 HD09333-01 to E. L. Cooper.     

TRPM7 regulates myosin IIA filament stability and protein localization by heavy chain phosphorylation

Deregulation of myosin II-based contractility contributes to the pathogenesis of human diseases, such as cancer, which underscores the necessity for tight spatial and temporal control of myosin II activity. Recently, we demonstrated that activation of the mammalian α-kinase TRPM7 inhibits myosin II-based contractility in a Ca²⁺- and kinase-dependent manner. However, the molecular mechanism is poorly defined. Here, we demonstrate that TRPM7 phosphorylates the COOH-termini of both mouse and human myosin IIA heavy chains—the COOH-terminus being a region that is critical for filament stability. Phosphorylated residues were mapped to Thr1800, Ser1803 and Ser1808. Mutation of these residues to alanine and that to aspartic acid lead to an increase and a decrease, respectively, in myosin IIA incorporation into the actomyosin cytoskeleton and accordingly affect subcellular localization. In conclusion, our data demonstrate that TRPM7 regulates myosin IIA filament stability and localization by phosphorylating a short stretch of amino acids within the α-helical tail of the myosin IIA heavy chain.