Isolation and characterisation of a NBS-LRR resistance gene analogue from pearl millet

Plant resistance (R) proteins belonging to nucleotide-binding site–leucine-rich repeat (NBS–LRR) family are mainly involved in recognition of effectors secreted by pathogens. Pearl millet [Pennisetum glaucum (L.) R.Br] is one of the most drought tolerant cereals, staple food crop of the semi-arid tropics but is highly susceptible to the downy mildew disease caused by oomycetous Sclerospora graminicola (Sacc) schroet. Earlier studies have identified several resistance gene analogues (RGAs) in pearl millet which may be involved in resistance against downy mildew. Of these, a clone RGPM213 was shown to have more than 60% identity with R-proteins coding for NBS–LRR-like protein kinase. The exact nature and function of the R-protein encoded by this gene was not known. In the present study, the cDNA of RGPM213 encompassing NBS–LRR region was inserted into an expression vector pRSET-A and transformed into BL21 E.coli cells. The expressed recombinant fusion protein with a His tag was purified using nickel affinity purification and it had a molecular weight of 35 kDa on SDS-PAGE. Immunoaffinity purification using antibodies raised against this recombinant R-protein identified two proteins of molecular weights 55 kDa and 66 kDa from pearl millet seedling extracts. Peptide mass fingerprinting of these proteins followed by homology search in database revealed similarity of the 55 kDa protein with a protein kinase from Brassica oleracia containing serine/ threonine kinase domain.     

Extraskeletal myxoid chondrosarcoma of the chest wall masquerading as a breast tumor. A case report

BACKGROUND: Extraskeletal myxoid chondrosarcoma is a rare tumor that usually occurs in the soft tissues of extremities. Cytologic features of chondrosarcoma arising from a rib and presenting as a breast mass were reported by Molyneux et al in 1995. However, to the best of our knowledge, the cytology of extraskeletal myxoid chondrosarcoma of the chest wall presenting as a breast mass has not been documented before. CASE: A 30-year-old female presented with left-sided chest pain and a hard lump in the breast of two months' duration. Fine needle aspiration cytology was done, and a possible diagnosis of mucinous carcinoma or mixed tumor of the breast was suggested, with advice to prepare a frozen section before undertaking a radical procedure. On imprint cytology and frozen section a diagnosis of extraskeletal myxoid chondrosarcoma was made and confirmed by histopathology and immunohistochemistry. CONCLUSION: It is rare for extraskeletal myxoid chondrosarcoma to occur in the chest wall. This problem is compounded by the fact that cells of extraskeletal myxoid chondrosarcoma which resemble epithelial cells, can very closely mimic some malignant breast tumors.     

A rapid progressor-specific variant clone of simian immunodeficiency virus replicates efficiently in vivo only in the absence of immune responses

A subset of simian immunodeficiency virus (SIV)-infected macaques progresses rapidly to disease with transient SIV-specific immune responses and high viral loads. Unique SIV variants with convergent Env mutations evolve in these rapid progressor (RP) macaques. To address the pathogenic significance of RP-specific variants, we generated infectious molecular clones from the terminal-phase plasma of an RP macaque. Inoculation of macaques with a representative clone, SIVsmH635FC, resulted in a persistent viremia, comparable to that produced by pathogenic SIVsmE543-3, and a chronic disease with progressive loss of CD4(+) T cells. However, SIVsmH635FC did not reproduce the rapid-disease phenomenon. Molecular analyses of viruses from these macaques revealed rapid reversion to the wild-type SIVsmE543-3 sequence at two RP-specific sites and slower reversion at another three sites. SIVsmH635FC infection was not sufficient to cause rapid progression even following coinoculation with SIVsmE543-3, despite acute depletion of memory CD4(+) T cells. SIVsmH635FC competed efficiently during primary infection in the coinoculated macaques, but SIVsmE543-3 predominated after the development of SIV-specific immune responses. These data suggest that the replication fitness of the RP variant was similar to that of SIVsmE543-3 in a na?ve host; however, SIVsmH635FC was at a disadvantage following the development of SIV-specific immune responses. Consistent with these findings, neutralization assays revealed that SIVsmH635FC was highly sensitive to neutralization but that the parental SIVsmE543-3 strain was highly resistant. This study suggests that the evolution of RP-specific variants is the result of replication in a severely immunocompromised host, rather than the direct cause of rapid progression.     

Cryptococcal lipid metabolism: phospholipase B1 is implicated in transcellular metabolism of macrophage-derived lipids

Cryptococci survive and replicate within macrophages and can use exogenous arachidonic acid for the production of eicosanoids. Phospholipase B1 (PLB1) has a putative, but uninvestigated, role in these processes. We have shown that uptake and esterification of radiolabeled arachidonic, palmitic, and oleic acids by the Cryptococcus neoformans var. grubii H99 wild-type strain and its PLB1 deletion mutant strain (the Deltaplb1 strain) are independent of PLB1, except under hyperosmolar stress. Similarly, PLB1 was required for metabolism of 1-palmitoyl lysophosphatidylcholine (LysoPC), which is toxic to eukaryotic cell membranes, under hyperosmolar conditions. During both logarithmic and stationary phases of growth, the physiologically relevant phospholipids, dipalmitoyl phosphatidylcholine (DPPC) and dioleoyl phosphatidylcholine, were taken up and metabolized via PLB1. Exogenous DPPC did not enhance growth in the presence of glucose as a carbon source but could support it for at least 24 h in glucose-free medium. Detoxification of LysoPC by reacylation occurred in both the H99 wild-type and the Deltaplb1 strains in the presence of glucose, but PLB1 was required when LysoPC was the sole carbon source. This indicates that both energy-independent (via PLB1) and energy-dependent transacylation pathways are active in cryptococci. Phospholipase A(1) activity was identified by PLB1-independent degradation of 1-palmitoyl-2-arachidonoyl phosphatidylcholine, but the arachidonoyl LysoPC formed was not detoxified by reacylation. Using the human macrophage-like cell line THP-1, we demonstrated the PLB1-dependent incorporation of macrophage-derived arachidonic acid into cryptococcal lipids during cryptococcus-phagocyte interaction. This pool of arachidonate can be sequestered for eicosanoid production by the fungus and/or suppression of host phagocytic activity, thus diminishing the immune response.     

Recombination-mediated changes in coreceptor usage confer an augmented pathogenic phenotype in a nonhuman primate model of HIV-1-induced AIDS

Evolution of the env gene in transmitted R5-tropic human immunodeficiency virus type 1 (HIV-1) strains is the most widely accepted mechanism driving coreceptor switching. In some infected individuals, however, a shift in coreceptor utilization can occur as a result of the reemergence of a cotransmitted, but rapidly controlled, X4 virus. The latter possibility was studied by dually infecting rhesus macaques with X4 and R5 chimeric simian simian/human immunodeficiency viruses (SHIVs) and monitoring the replication status of each virus using specific primer pairs. In one of the infected monkeys, both SHIVs were potently suppressed by week 12 postinoculation, but a burst of viremia at week 51 was accompanied by an unrelenting loss of total CD4+ T cells and the development of clinical disease. PCR analyses of plasma viral RNA indicated an env gene segment containing the V3 region from the inoculated X4 SHIV had been transferred into the genetic background of the input R5 SHIV by intergenomic recombination, creating an X4 virus with novel replicative, serological, and pathogenic properties. These results indicate that the effects of retrovirus recombination in vivo can be functionally profound and may even occur when one of the recombination participants is undetectable in the circulation as cell-free virus.     

Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity

Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) is mutated frequently in gliomas and represents a potential target for cancer therapies. ATRX is known to function as a histone chaperone that helps incorporate histone variant, H3.3, into the genome. Studies have implicated ATRX in key DNA damage response (DDR) pathways but a distinct role in DNA repair has yet to be fully elucidated. To further investigate the function of ATRX in the DDR, we created isogenic wild-type (WT) and ATRX knockout (KO) model cell lines using CRISPR-based gene targeting. These studies revealed that loss of ATRX confers sensitivity to poly(ADP)-ribose polymerase (PARP) inhibitors, which was linked to an increase in replication stress, as detected by increased activation of the ataxia telangiectasia and Rad3-related (ATR) signaling axis. ATRX mutations frequently co-occur with mutations in isocitrate dehydrogenase-1 and -2 (IDH1/2), and the latter mutations also induce HR defects and PARP inhibitor sensitivity. We found that the magnitude of PARP inhibitor sensitivity was equal in the context of each mutation alone, although no further sensitization was observed in combination, suggesting an epistatic interaction. Finally, we observed enhanced synergistic tumor cell killing in ATRX KO cells with ATR and PARP inhibition, which is commonly seen in HR-defective cells. Taken together, these data reveal that ATRX may be used as a molecular marker for DDR defects and PARP inhibitor sensitivity, independent of IDH1/2 mutations. These data highlight the important role of common glioma-associated mutations in the regulation of DDR, and novel avenues for molecularly guided therapeutic intervention.     

Stress induced lipid production in Chlorella vulgaris: Relationship with specific intracellular reactive species levels

Microalgae have significant potential to be an important alternative energy source, but the challenges to the commercialization of bio‐oil from microalgae need to be overcome for the potential to be realized. The application of stress can be used to improve bio‐oil yields from algae. Nevertheless, the understanding of stress effects is fragmented due to the lack of a suitable, direct quantitative marker for stress. The lack of understanding seems to have limited the development of stress based strategies to improve bio‐oil yields, and hence the commercialization of microalgae‐based bio‐oil. In this study, we have proposed and used the specific intracellular reactive species levels (siROS) particularly hydroxyl and superoxide radical levels, separately, as direct, quantitative, markers for stress, irrespective of the type of stress induced. Although ROS reactions are extremely rapid, the siROS level can be assumed to be at pseudo‐steady state compared to the time scales of metabolism, growth and production, and hence they can be effective stress markers at particular time points. Also, the specific intracellular (si‐) hydroxyl and superoxide radical levels are easy to measure through fluorimetry. Interestingly, irrespective of the conditions employed in this study, that is, nutrient excess/limitation or different light wavelengths, the cell concentrations are correlated to the siROS levels in an inverse power law fashion. The composite plots of cell concentration (y) and siROS (x) yielded the correlations of y = k₁ · x^?0.7 and y = k₂ · x^?0.79, for si‐hydroxyl and si‐superoxide radical levels, respectively. The specific intracellular (si‐) neutral lipid levels, which determine the bio‐oil productivity, are related in a direct power law fashion to the specific hydroxyl radical levels. The composite plot of si‐neutral lipid levels (z) and si‐hydroxyl radical level (x) yielded a correlation of z = k₃ · x^0.65. More interestingly, a nutrient shift caused a significant change in the sensitivity of neutral lipid accumulation to the si‐hydroxyl radical levels. Biotechnol. Bioeng. 2013; 110: 1627–1636. © 2013 Wiley Periodicals, Inc.     

Loss of ��-Catenin Decreases the Strength of Single E-cadherin Bonds between Human Cancer Cells

The progression of several human cancers correlates with the loss of cytoplasmic protein α-catenin from E-cadherin-rich intercellular junctions and loss of adhesion. However, the potential role of α-catenin in directly modulating the adhesive function of individual E-cadherin molecules in human cancer is unknown. Here we use single-molecule force spectroscopy to probe the tensile strength, unstressed bond lifetime, and interaction energy between E-cadherins expressed on the surface of live human parental breast cancer cells lacking α-catenin and these cells where α-catenin is re-expressed. We find that the tensile strength and the lifetime of single E-cadherin/E-cadherin bonds between parental cells are significantly lower over a wide range of loading rates. Statistical analysis of the force displacement spectra reveals that single cadherin bonds between cancer cells feature an exceedingly low energy barrier against tensile forces and low molecular stiffness. Disassembly of filamentous actin using latrunculin B has no significant effect on the strength of single intercellular E-cadherin bonds. The absence of α-catenin causes a dominant negative effect on both global cell-cell adhesion and single E-cadherin bond strength. These results suggest that the loss of α-catenin alone drastically reduces the adhesive force between individual cadherin pairs on adjoining cells, explain the global loss of cell adhesion in human breast cancer cells, and show that the forced expression of α-catenin in cancer cells can restore both higher intercellular avidity and intercellular E-cadherin bond strength.The reduction of intercellular adhesion in a solid tumor is a critical step in the progression of tumor cells to metastasis (1). How normal cells lose their ability to form strong adhesions within a tissue is not well understood (2, 3). The loss of adhesion between adjoining epithelial cells and the ensuing onset of metastasis occur through an epithelial-to-mesenchymal transition that often correlates with the loss of cytoplasmic protein α-catenin and a poor prognosis in a wide range of cancers, including breast (4), esophageal (5), gastric (6, 7), cervical (8), and colorectal cancer (9). In normal epithelial tissues, α-catenin localizes to junctions that organize at the interface between adjacent epithelial cells through clustering of cell surface adhesion transmembrane molecule cadherin and its association to the cytoskeleton (10, 11). On the extracellular side, structural studies suggest that cadherin molecules form molecular pairs that interact with cadherin pairs on an adjacent cell through their distal Ca²⁺-binding domains (12). On the intracellular side, cadherin pairs are connected to the cytoskeleton network through specific linker proteins. Until recently it was believed that one critical linker protein between the cytoplasmic domain of cadherin and the actin cytoskeleton was α-catenin, because it can both bind filamentous actin (F-actin) and E-cadherin through β-catenin (13, 14). However, a recent study indicates that α-catenin can either bind the E-cadherin-β-catenin complex as monomer or cross-link actin filaments as homodimer but cannot bind both E-cadherin-β-catenin and F-actin simultaneously (15). Therefore, whether the loss of α-catenin plays a direct role in the loss of adhesion in human cancer cells is unclear.Our recent data using engineered Chinese hamster ovarian cells suggest that α-catenin mediates the rapid strengthening of individual intercellular E-cadherin/E-cadherin bonds following initial molecular recognition between cells bearing E-cadherin molecules (16). Furthermore, α-catenin mediates the formation of additional E-cadherin/E-cadherin bonds once a first bond is formed between adjoining cells to form a nascent intercellular junction (16). Here we hypothesize that the loss of cytoplasmic protein α-catenin in human cancer cells greatly affects the ability of E-cadherin molecules on the surface of these cells to form firm adhesion by reducing the strength of individual intercellular E-cadherin/E-cadherin bonds.Our strategy is to compare parental breast cancer cells that lack α-catenin (MDA-MB-468 cells; denoted here MDA468) with these cells when α-catenin is introduced and exploit high resolution live cell single-molecule force spectroscopy (17) to probe the strength of individual E-cadherin/E-cadherin bonds between adjacent cells (18). The cells are juxtaposed for a controlled time of contact, the probability of successful interactions is subsequently measured, and the mechanical properties (tensile strength, molecular stiffness, and reactive compliance) and biochemical properties (interaction energy, dissociation rate, and bond lifetime) of single intercellular E-cadherin/E-cadherin bonds are analyzed.Our main hypothesis cannot be readily tested using purified proteins. Our ability to measure molecular interactions between live cells (17) rather than recombinant proteins ensures that the proper orientation of cadherin on the cell surfaces and its post-translational modifications are physiological. Moreover, using living cells ensures that the cytoplasmic domain of transmembrane receptors (here human E-cadherin) can interact with cytoplasmic proteins (in particular β-catenin and α-catenin), thereby allowing cell signaling pathways that can influence cell adhesion to function normally.     

Differential regulation of dendrite complexity by AMPA receptor subunits GluR1 and GluR2 in motor neurons

Activity-dependent developmental mechanisms in many regions of the central nervous system are thought to be responsible for shaping dendritic architecture and connectivity, although the molecular mechanisms underlying these events remain obscure. Since AMPA glutamate receptors are developmentally regulated in spinal motor neurons, we have investigated the role of activation of AMPA receptors in dendritic outgrowth of spinal motor neurons by overexpression of two subunits, GluR1 and GluR2, and find that dendrite outgrowth is differentially controlled by expression of these subunits. Overexpression of GluR1 was associated with greater numbers of filopodia, and an increase in the length and complexity of dendritic arbor. In contrast, GluR2 expression did not alter dendritic complexity, but was associated with a moderate increase in length of arbor, and decreased numbers of filopodia. Neither GluR1 nor GluR2 had any effect on the motility of filopodia. In addition, GluR1 but not GluR2 expression increased the density of dendritic puncta incorporating a GFP-labeled PSD95, suggesting that GluR1 may mediate its effect in part by augmenting the number of excitatory synapses within motor neuron dendrites. Together these results suggest that in spinal motor neurons, AMPA receptors composed of GluR1 subunits may facilitate neurotrophic mechanisms in these neurons, permitting sustained dendrite outgrowth and synaptogenesis, whereas expression of AMPA receptors containing GluR2 acts to preserve existing dendritic arbor. Thus, the observed downregulation of GluR1 in motor neurons during postnatal development may limit the formation of new dendrite segments and synapses, promoting stabilized synaptic connectivity.     

Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1

The diacylglycerol kinase (DGK) enzymes function as regulators of intracellular signaling by altering the levels of the second messengers, diacylglycerol and phosphatidic acid. The DGK delta and eta isozymes possess a common protein-protein interaction module known as a sterile alpha-motif (SAM) domain. In DGK delta, SAM domain self-association inhibits the translocation of DGK delta to the plasma membrane. Here we show that DGK delta SAM forms a polymer and map the polymeric interface by a genetic selection for soluble mutants. A crystal structure reveals that DGKSAM forms helical polymers through a head-to-tail interaction similar to other SAM domain polymers. Disrupting polymerization by polymer interface mutations constitutively localizes DGK delta to the plasma membrane. Thus, polymerization of DGK delta regulates the activity of the enzyme by sequestering DGK delta in an inactive cellular location. Regulation by dynamic polymerization is an emerging theme in signal transduction.