ResearchPad - addendum https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Editorial Expression of Concern: IRE1a constitutes a negative feedback loop with BMP2 and acts as a novel mediator in modulating osteogenic differentiation]]> https://www.researchpad.co/article/N00dfcb64-417f-400c-93ec-52d0d18014cf <![CDATA[Editorial Expression of Concern: Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population]]> https://www.researchpad.co/article/Nebe43c54-0d20-4127-8972-6102d85edac8 ]]> <![CDATA[Dissemination and Continuous Improvement of a CTSA-based Software Platform, SPARCRequest©, Using an Open Source Governance Model – ADDENDUM]]> https://www.researchpad.co/article/N083bec71-5172-4149-9f9b-a800e8be6040 ]]> <![CDATA[Addendum: Zhang, C., et al. Pulsed Laser-Assisted Helium Ion Nanomachining of Monolayer Graphene—Direct-Write Kirigami Patterns. Nanomaterials 2019, 9, 1394]]> https://www.researchpad.co/article/N5439b1ba-1f37-4ed4-9bf2-8334780a0c22 ]]> <![CDATA[Addendum: Zurob, E., et al. Inhibition of Wild Enterobacter cloacae Biofilm Formation by Nanostructured Graphene- and Hexagonal Boron Nitride-Coated Surfaces. Nanomaterials 2019, 9, 49]]> https://www.researchpad.co/article/Na83123d4-3501-4bb3-b03f-8e1ca29b07c5 ]]> <![CDATA[Global Science Meets Ethnic Diversity: Ian McGonigle interviews GenomeAsia100k Scientific Chairman Stephan Schuster–ADDENDUM]]> https://www.researchpad.co/article/N09f55715-ac2c-428d-a91a-76f8d18844ce ]]> <![CDATA[Serine-rich repeat proteins from gut microbes]]> https://www.researchpad.co/article/Na43fd9aa-5d7e-4dab-b442-4552ee99abc7

ABSTRACT

Serine-rich repeat proteins (SRRPs) have emerged as an important group of cell surface adhesins found in a growing number of Gram-positive bacteria. Studies focused on SRRPs from streptococci and staphylococci demonstrated that these proteins are O-glycosylated on serine or threonine residues and exported via an accessory secretion (aSec) system. In pathogens, these adhesins contribute to disease pathogenesis and represent therapeutic targets. Recently, the non-canonical aSec system has been identified in the genomes of gut microbes and characterization of their associated SRRPs is beginning to unfold, showing their role in mediating attachment and biofilm formation. Here we provide an update of the occurrence, structure, and function of SRRPs across bacteria, with emphasis on the molecular and biochemical properties of SRRPs from gut symbionts, particularly Lactobacilli. These emerging studies underscore the range of ligands recognized by these adhesins and the importance of SRRP glycosylation in the interaction of gut microbes with the host.

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<![CDATA[“I will survive”: A tale of bacteriophage-bacteria coevolution in the gut]]> https://www.researchpad.co/article/5c79b849d5eed0c4841f0130

ABSTRACT

Viruses that infect bacteria, or bacteriophages, are among the most abundant entities in the gut microbiome. However, their role and the mechanisms by which they infect bacteria in the intestinal tract remain poorly understood. We recently reported that intestinal bacteria are an evolutionary force, driving the expansion of the bacteriophage host range by boosting the genetic variability of these viruses. Here, we expand these observations by studying antagonistic bacteriophage-bacteria coevolution dynamics and revealing that bacterial genetic variability is also increased under the pressure of bacteriophage predation. We propose a model showing how the expansion of bacteriophage-bacteria infection networks is relative to the opportunities for coevolution encountered in the intestinal tract. Our data suggest that predator-prey dynamics are perpetuated and differentiated in parallel, to generate and maintain intestinal microbial diversity and equilibrium.

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<![CDATA[Addendum for Euro Surveill. 2018;23(10)]]> https://www.researchpad.co/article/5c6db0fdd5eed0c48450ca5f ]]> <![CDATA[Phytosiderophores revisited: 2′-deoxymugineic acid-mediated iron uptake triggers nitrogen assimilation in rice (Oryza sativa L.) seedlings]]> https://www.researchpad.co/article/5bc4789640307c32b55bc9fc

Poaceae plants release phytosiderophores into the rhizosphere in order to chelate iron (Fe), which often exists in insoluble forms especially under high pH conditions. The impact of phytosiderophore treatment at the physiological and molecular levels in vivo remains largely elusive, although the biosynthesis of phytosiderophores and the transport of phytosiderophore-metal complexes have been well studied. We recently showed that the application of 30 μM of the chemically synthesized phytosiderophore 2′-deoxymugineic acid (DMA) was sufficient for apparent full recovery of otherwise considerably reduced growth of hydroponic rice seedlings at high pH. Moreover, unexpected induction of high-affinity nitrate transporter gene expression as well as nitrate reductase activity indicates that the nitrate response is linked to Fe homeostasis. These data shed light on the biological relevance of DMA not simply as a Fe chelator, but also as a trigger that promotes plant growth by reinforcing nitrate assimilation.

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<![CDATA[In situ analysis of epigenetic modifications in the chromatin of Brachypodium distachyon embryos]]> https://www.researchpad.co/article/5bc4de7740307c7a1d4e9f27

Epigenetic modifications of the chromatin structure are crucial for many biological processes and act on genes during the development and germination of seeds. The spatial distribution of 3 epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 was investigated in ‘matured,’ ‘dry,’ ‘imbibed” and ‘germinating’ embryos of a model grass, Brachypodium. Our results indicate that the patterns of epigenetic modification differ in the various types of tissues of embryos that were analyzed. Such a tissue-specific manner of these modifications may be linked to the switch of the gene expression profiles in various organs of the developing embryo.

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<![CDATA[Spondylocheirodysplastic Ehlers-Danlos syndrome (SCD-EDS) and the mutant zinc transporter ZIP13]]> https://www.researchpad.co/article/5af97fdc463d7e18874b4b75

The zinc transporter protein ZIP13 plays crucial roles in bone, tooth, and connective tissue development, and its dysfunction is responsible for the spondylocheirodysplastic form of Ehlers-Danlos syndrome (SCD-EDS, OMIM 612350). We recently reported that the pathogenic mutations in ZIP13 reduce its functional protein level by accelerating the protein degradation via the VCP-linked ubiquitin proteasome pathway, resulting in the disturbance of intracellular zinc homeostasis that appears to contribute to SCD-EDS pathogenesis. Finally, we implicate that possible therapeutic approaches for SCD-EDS would be based on regulating the degradation of the pathogenic mutant ZIP13 proteins.

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<![CDATA[Engineering low-temperature expression systems for heterologous production of cold-adapted enzymes]]> https://www.researchpad.co/article/5bd2bf84d5eed0c484dc3869

ABSTRACT

Production of psychrophilic enzymes in the commonly used mesophilic expression systems is hampered by low intrinsic stability of the recombinant enzymes at the optimal host growth temperatures. Unless strategies for low-temperature expression are advanced, research on psychrophilic enzymes may end up being biased toward those that can be stably produced in commonly used mesophilic host systems. Two main strategies are currently being explored for the development of low-temperature expression in bacterial hosts: (i) low-temperature adaption of existing mesophilic expression systems, and (ii) development of new psychrophilic hosts. These developments include genetic engineering of the expression cassettes to optimize the promoter/operator systems that regulate heterologous expression. In this addendum we present our efforts in the development of such low-temperature expression systems, and speculate about future advancements in the field and potential applications.

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<![CDATA[Botulinum toxin A modifies nociceptive withdrawal reflex in subacute stroke patients]]> https://www.researchpad.co/article/5c3687add5eed0c4841ff6ef ]]> <![CDATA[Ranolazine inhibits shear sensitivity of endogenous Na+ current and spontaneous action potentials in HL-1 cells]]> https://www.researchpad.co/article/5ac8bf89463d7e53341ec660

NaV1.5 is a mechanosensitive voltage-gated Na+ channel encoded by the gene SCN5A, expressed in cardiac myocytes and required for phase 0 of the cardiac action potential (AP). In the cardiomyocyte, ranolazine inhibits depolarizing Na+ current and delayed rectifier (IKr) currents. Recently, ranolazine was also shown to be an inhibitor of NaV1.5 mechanosensitivity. Stretch also accelerates the firing frequency of the SA node, and fluid shear stress increases the beating rate of cultured cardiomyocytes in vitro. However, no cultured cell platform exists currently for examination of spontaneous electrical activity in response to mechanical stimulation. In the present study, flow of solution over atrial myocyte-derived HL-1 cultured cells was used to study shear stress mechanosensitivity of Na+ current and spontaneous, endogenous rhythmic action potentials. In voltage-clamped HL-1 cells, bath flow increased peak Na+ current by 14 ± 5%. In current-clamped cells, bath flow increased the frequency and decay rate of AP by 27 ± 12% and 18 ± 4%, respectively. Ranolazine blocked both responses to shear stress. This study suggests that cultured HL-1 cells are a viable in vitro model for detailed study of the effects of mechanical stimulation on spontaneous cardiac action potentials. Inhibition of the frequency and decay rate of action potentials in HL-1 cells are potential mechanisms behind the antiarrhythmic effect of ranolazine.

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<![CDATA[Resistance to pathogens in terpene down-regulated orange fruits inversely correlates with the accumulation of D-limonene in peel oil glands]]> https://www.researchpad.co/article/5bc4789e40307c32b55bc9ff

Volatile organic compounds (VOCs) are secondary metabolites acting as a language for the communication of plants with the environment. In orange fruits, the monoterpene D-limonene accumulates at very high levels in oil glands from the peel. Drastic down-regulation of D-limonene synthase gene expression in the peel of transgenic oranges harboring a D-limonene synthase transgene in antisense (AS) configuration altered the monoterpene profile in oil glands, mainly resulting in reduced accumulation of D-limonene. This led to fruit resistance against Penicillium digitatum (Pd), Xanthomonas citri subsp. citri (Xcc) and other specialized pathogens. Here, we analyze resistance to pathogens in independent AS and empty vector (EV) lines, which have low, medium or high D-limonene concentrations and show that the level of resistance is inversely related to the accumulation of D-limonene in orange peels, thus explaining the need of high D-limonene accumulation in mature oranges in nature for the efficient attraction of specialized microorganism frugivores.

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<![CDATA[Optimization of saccharification potential of recombinant xylanase from Bacillus licheniformis]]> https://www.researchpad.co/article/5c0dcb62d5eed0c484cf9de8

ABSTRACT

Saccharification potential of xylanase enzyme cloned from Bacillus licheniformis into E. coli BL21 (DE3) was evaluated against plant biomass for the production of bioethanol. The expression of cloned gene was studied and conditions were optimized for its large scale production. The parameters effecting enzyme production were examined in a fermenter. Recombinant xylanase has the ability to breakdown birchwood xylan to release xylose as well as the potential to treat plant biomass, such as wheat straw, rice straw, and sugarcane bagass. The saccharification ability of this enzyme was optimized by studying various parameters. The maximum saccharification percentage (84%) was achieved when 20 units of recombinant xylanase were used with 8% sugarcane bagass at 50°C and 120 rpm after 6 hours of incubation. The results indicated that the bioconversion of natural biomass by recombinant xylanase into simple sugars can be used for biofuel (bioethanol) production. This process can replace the use of fossil fuels, and the use of bioethanol can significantly reduce the emission of toxic gases. Future directions regarding pre-treatment of cellulosic and hemicellulosic biomass and other processes that can reduce the cost and enhance the yield of biofuels are briefly discussed.

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<![CDATA[Non-inductive conditions expose the cryptic bract of flower phytomeres in Arabidopsis thaliana]]> https://www.researchpad.co/article/5b2a71b0463d7e356096e573

The aerial plant architecture is built by phytomeres which are metameric units, each composed of a stem segment (internode) and a leaf with axillary meristem (node). In Arabidopsis thaliana, fully developed flower phytomeres lack the leaf even if they temporarily exhibit a cryptic bract (CB) during early development. Recently, we demonstrated that the CB becomes more prominent under non-inductive short-day conditions. However, a full outgrowth as cauline leaf is prevented by Polycomb-group (Pc-G) proteins which silence the MADS gene FLOWERING LOCUS C (FLC) encoding a repressor of FLOWERING LOCUS T (FT). Also the loss of SHORT VEGETATIVE PHASE (SVP) supresses ectopic leaves at the base of Pc-G deficient pedicels. Here we present new expression data of flowering genes LEAFY (LFY) and TWIN SISTER OF FT (TSF) and the re-analysis of morphological changes in Pc-G deficient plants suggesting that the specifications of CB and floral meristem (FM) are separated in time.

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<![CDATA[mVps45 knockdown selectively modulates VAMP expression in 3T3-L1 adipocytes]]> https://www.researchpad.co/article/5af23774463d7e3b583c1db5

Insulin stimulates the delivery of glucose transporter-4 (GLUT4)-containing vesicles to the surface of adipocytes. Depletion of the Sec1/Munc18 protein mVps45 significantly abrogates insulin-stimulated glucose transport and GLUT4 translocation. Here we show that depletion of mVps45 selectively reduced expression of VAMPs 2 and 4, but not other VAMP isoforms. Although we did not observe direct interaction of mVps45 with any VAMP isoform; we found that the cognate binding partner of mVps45, Syntaxin 16 associates with VAMPs 2, 4, 7 and 8 in vitro. Co-immunoprecipitation experiments in 3T3-L1 adipocytes revealed an interaction between Syntaxin 16 and only VAMP4. We suggest GLUT4 trafficking is controlled by the coordinated expression of mVps45/Syntaxin 16/VAMP4, and that depletion of mVps45 regulates VAMP2 levels indirectly, perhaps via reduced trafficking into specialized subcellular compartments.

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<![CDATA[Addendum: Shiue, I.; et al. 2014 Future Earth Young Scientists Conference on Integrated Science and Knowledge Co-Production for Ecosystems and Human Well-Being. Int. J. Environ. Res. Public Health 2014, 11, 11553–11558]]> https://www.researchpad.co/article/5ae437ef463d7e051e11bb67 ]]>