Utility of Host Delivered RNAi of Two FMRF Amide Like Peptides,flp-14 and flp-18, for the Management of Root Knot Nematode,Meloidogyne incognita

Root knot nematode, Meloidogyne incognita, is an obligate sedentary endoparasite that infects a large number of crop species and causes substantial yield losses. Non-chemical based control strategies for these nematodes are gaining importance. In the present study, we have demonstrated the significance of two FMRFamide like peptide genes (flp-14 and flp-18) for infection and development of resistance to M. incognita through host-derived RNAi. The study demonstrated both in vitro and in planta validation of RNAi-induced silencing of the two genes cloned from J2 stage of M. incognita. In vitro silencing of both the genes interfered with nematode migration towards the host roots and subsequent invasion into the roots. Transgenic tobacco lines were developed with RNAi constructs of flp-14 and flp-18 and evaluated against M. incognita. The transformed plants did not show any visible phenotypic variations suggesting the absence of any off-target effects. Bioefficacy studies with deliberate challenging of M. incognita resulted in 50-80% reduction in infection and multiplication confirming the silencing effect. We have provided evidence for in vitro and in planta silencing of the genes by expression analysis using qRT-PCR. Thus the identified genes and the strategy can be used as a potential tool for the control of M. incognita. This is the first ever report that has revealed the utility of host delivered RNAi of flps to control M. incognita. The strategy can also be extended to other crops and nematodes.     

Understanding and modeling retention of mammalian cells in fluidized bed centrifuges

Within the last decade, fully disposable centrifuge technologies, fluidized‐bed centrifuges (FBC), have been introduced to the biologics industry. The FBC has found a niche in cell therapy where it is used to collect, concentrate, and then wash mammalian cell product while continuously discarding centrate. The goal of this research was to determine optimum FBC conditions for recovery of live cells, and to develop a mathematical model that can assist with process scaleup. Cell losses can occur during bed formation via flow channels within the bed. Experimental results with the kSep400 centrifuge indicate that, for a given volume processed: the bed height (a bed compactness indicator) is affected by RPM and flowrate, and dead cells are selectively removed during operation. To explain these results, two modeling approaches were used: (i) equating the centrifugal and inertial forces on the cells (i.e., a force balance model or FBM) and (ii) a two‐phase computational fluid dynamics (CFD) model to predict liquid flow patterns and cell retention in the bowl. Both models predicted bed height vs. time reasonably well, though the CFD model proved more accurate. The flow patterns predicted by CFD indicate a Coriolis‐driven flow that enhances uniformity of cells in the bed and may lead to cell losses in the outflow over time. The CFD‐predicted loss of viable cells and selective removal of the dead cells generally agreed with experimental trends, but did over‐predict dead cell loss by up to 3‐fold for some of the conditions. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1520–1530, 2016     

Effects of GsMTx4 on bacterial mechanosensitive channels in inside-out patches from giant spheroplasts

GsMTx4 is a 34-residue peptide isolated from the tarantula Grammostola spatulata folded into an inhibitory cysteine knot and it selectively affects gating of some mechanosensitive channels. Here we report the effects of cytoplasmic GsMTx4 on the two bacterial channels, MscS and MscL, in giant Escherichia coli spheroplasts. In excised inside-out patches, GsMTx4 sensitized both channels to tension by increasing the opening rate and decreasing the closing rate. With ascending and descending pressure ramps, GsMTx4 increased the gating hysteresis for MscS, a consequence of slower gating kinetics. Quantitative kinetic analysis of the primary C↔O transition showed that the hysteresis is a result of the decreased closing rate. The gating barrier location relative to the open state energy well was unaffected by GsMTx4. A reconstructed energy profile suggests that the peptide prestresses the resting state of MscS, lowering the net barrier to opening and stabilizes the open conformation by ∼8 kT. In excised patches, both MscL and MscS exhibit reversible adaptation, a process separable from inactivation for MscS. GsMTx4 decreased the rate of reversible adaptation for both channels and the MscS recovery rate from the inactivation. These measurements support a mechanism where GsMTx4 binds to the lipid interface of the channel, increasing the local stress that is sensed by the channels and stabilizing the expanded conformations.     

Lentiviral reporter constructs for fluorescence tracking of the temporospatial pattern of Smad3 signaling

Canonical TGF-beta is involved in cell differentiation, tissue maintenance, and wound healing, but also plays a central role in the pathogenesis of diseases such as cancer Here we describe a lentivirus-based reporter vector system expressing green fluorescent protein (GFP) or red fluorescent protein (RFP) under the control of a Smad3-responsive element (CAGA)12 that allows observation of the temporospatial pattern of endogeneous Smad3-mediated signaling on a cellular level. Use of this method will be valuable to identify cells with active Smad3 signaling and investigate the role of endogenous Smad3 signaling in complex systems such as co-cultures in vitro, or in tumors during tumor cell invasion and metastasis in vivo.     

Observations on sporozoite detection in naturally infected sibling species of the <Emphasis Type="Italic">Anopheles culicifacies</Emphasis> complex and variant of <Emphasis Type="Italic">Anopheles stephensi</Emphasis> in India

Sporozoites were detected in naturally infected sibling species of the primary rural vector Anopheles culicifacies complex in two primary health centres (PHCs) and a variant of the urban vector Anopheles stephensi in Mangalore city, Karnataka, south India while carrying out malaria outbreak investigations from 1998–2006. Sibling species of An. culicifacies were identified based on the banding patterns on ovarian polytene chromosomes, and variants of An. stephensi were identified based on the number of ridges on the egg floats. Sporozoites were detected in the salivary glands by the dissection method. Of the total 334 salivary glands of An. culicifacies dissected, 17 (5.08%) were found to be positive for sporozoites. Of the 17 positive samples, 11 were suitable for sibling species analysis; 10 were species A (an efficient vector) and 1 was species B (a poor vector). Out of 46 An. stephensi dissected, one was sporozoite positive and belonged to the type form (an efficient vector). In malaria epidemiology this observation is useful for planning an effective vector control programme, because each sibling species/variant differs in host specificity, susceptibility to malarial parasites, breeding habitats and response to insecticides.     

The membrane lateral pressure-perturbing capacity of parabens and their effects on the mechanosensitive channel directly correlate with hydrophobicity

Lipid bilayers provide a natural anisotropic environment for membrane proteins and can serve as apolar reservoirs for lipid-derived second messengers or lipophilic drugs. Partitioning of lipophilic agents changes the lateral pressure distribution in the bilayer, affecting integral proteins. p-Hydroxybenzoic acid esters (parabens) are amphipathic compounds widely used as food and cosmetics preservatives, but the mechanisms of their broad antibacterial action are unknown. Here we describe effects of ethyl, propyl, and butyl parabens on the gating of the bacterial mechanosensitive channel of small conductance (MscS) and compare them with the surface activity and lateral pressure changes measured in lipid monolayers in the presence of these substances. Near the bilayer-monolayer equivalence pressure of 35 mN/m, ethyl, propyl, or butyl paraben present in the subphase at 1 mM increased the surface pressure of the monolayer by 5, 12.5, or 20%, respectively. No spontaneous activation of MscS channels was observed in patch-clamp experiments with parabens added from either the cytoplasmic or periplasmic side. Increasing concentrations of parabens on the cytoplasmic side of excised patches shifted activation curves of MscS toward higher tensions. A good correlation between the pressure increases in monolayers and shifts in activation midpoints in patch-clamp experiments suggested that the more hydrophobic parabens partition more strongly into the lipid and exert larger effects on channel gating through changes in lateral pressure. We show that cytoplasmically presented ethyl or butyl parabens both hasten the process of desensitization of MscS and influence inactivation differently. The higher rate of desensitization is likely due to increased lateral pressure in the cytoplasmic leaflet surrounding the gate. Neither of the parabens strongly affects the rate of recovery and does not seem to penetrate the TM2-TM3 interhelical clefts in MscS. We conclude that the bacterial mechanosensitive channel MscS provides a sensitive readout of lateral membrane pressure exerted by amphipathic molecules but may not be the primary target for the parabens in their antimicrobial activity.     

L<Subscript>2</Subscript>-norm multiple kernel learning and its application to biomedical data fusion

Background  

This paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learning (MKL) such as L _∞, L ₁, and L ₂ MKL. In particular, L ₂ MKL is a novel method that leads to non-sparse optimal kernel coefficients, which is different from the sparse kernel coefficients optimized by the existing L _∞ MKL method. In real biomedical applications, L ₂ MKL may have more advantages over sparse integration method for thoroughly combining complementary information in heterogeneous data sources.