4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

Background

Synthetic biology is a discipline that includes making life forms artificially from chemicals. Here, a DNA molecule was enzymatically synthesized in vitro from DNA templates made from oligonucleotides representing the text of the first Tobacco mosaic virus (TMV) sequence elucidated in 1982. No infectious DNA molecule of that seminal reference sequence exists, so the goal was to synthesize it and then build viral chimeras.

Results

RNA was transcribed from synthetic DNA and encapsidated with capsid protein in vitro to make synthetic virions. Plants inoculated with the virions did not develop symptoms. When two nucleotide mutations present in the original sequence, but not present in most other TMV sequences in GenBank, were altered to reflect the consensus, the derivative synthetic virions produced classic TMV symptoms. Chimeras were then made by exchanging TMV capsid protein DNA with Tomato mosaic virus (ToMV) and Barley stripe mosaic virus (BSMV) capsid protein DNA. Virus expressing ToMV capsid protein exhibited altered, ToMV-like symptoms in Nicotiana sylvestris. A hybrid ORF6 protein unknown to nature, created by substituting the capsid protein genes in the virus, was found to be a major symptom determinant in Nicotiana benthamiana. Virus expressing BSMV capsid protein did not have an extended host range to barley, but did produce novel symptoms in N. benthamiana.

Conclusions

This first report of the chemical synthesis and artificial assembly of a plant virus corrects a long-standing error in the TMV reference genome sequence and reveals that unnatural hybrid virus proteins can alter symptoms unexpectedly.     

Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum

Clostridium thermocellum is an anaerobic thermophilic bacterium that grows efficiently on cellulosic biomass. This bacterium produces and secretes a highly active multienzyme complex, the cellulosome, that mediates the cell attachment to and hydrolysis of the crystalline cellulosic substrate. C. thermocellum can efficiently utilize only β-1,3 and β-1,4 glucans and prefers long cellodextrins. Since the bacterium can also produce ethanol, it is considered an attractive candidate for a consolidated fermentation process in which cellulose hydrolysis and ethanol fermentation occur in a single process. In this study, we have identified and characterized five sugar ABC transporter systems in C. thermocellum. The putative transporters were identified by sequence homology of the putative solute-binding lipoprotein to known sugar-binding proteins. Each of these systems is transcribed from a gene cluster, which includes an extracellular solute-binding protein, one or two integral membrane proteins, and, in most cases, an ATP-binding protein. The genes of the five solute-binding proteins were cloned, fused to His tags, overexpressed, and purified, and their abilities to interact with different sugars was examined by isothermal titration calorimetry. Three of the sugar-binding lipoproteins (CbpB to -D) interacted with different lengths of cellodextrins (G₂ to G₅), with disassociation constants in the micromolar range. One protein, CbpA, binds only cellotriose (G₃), while another protein, Lbp (laminaribiose-binding protein) interacts with laminaribiose. The sugar specificity of the different binding lipoproteins is consistent with the observed substrate preference of C. thermocellum, in which cellodextrins (G₃ to G₅) are assimilated faster than cellobiose.     

Direct interaction between the COG complex and the SM protein,Sly1, is required for Golgi SNARE pairing

The crucial roles of Sec1/Munc18 (SM)‐like proteins in membrane fusion have been evidenced in genetic and biochemical studies. SM proteins interact directly with SNAREs and contribute to SNARE pairing by a yet unclear mechanism. Here, we show that the SM protein, Sly1, interacts directly with the conserved oligomeric Golgi (COG) tethering complex. The Sly1–COG interaction is mediated by the Cog4 subunit, which also interacts with Syntaxin 5 through a different binding site. We provide evidence that disruption of Cog4–Sly1 interaction impairs pairing of SNAREs involved in intra‐Golgi transport thereby markedly attenuating Golgi‐to‐ER retrograde transport. These results highlight the mechanism by which SM proteins link tethering to SNAREpin assembly.     

Cell Type–dependent Requirement for PIP Box–regulated Cdt1 Destruction During S Phase

DNA synthesis–coupled proteolysis of the prereplicative complex component Cdt1 by the CRL4^Cdt2 E3 ubiquitin ligase is thought to help prevent rereplication of the genome during S phase. To directly test whether CRL4^Cdt2-triggered destruction of Cdt1 is required for normal cell cycle progression in vivo, we expressed a mutant version of Drosophila Cdt1 (Dup), which lacks the PCNA-binding PIP box (Dup^ΔPIP) and which cannot be regulated by CRL4^Cdt2. Dup^ΔPIP is inappropriately stabilized during S phase and causes developmental defects when ectopically expressed. Dup^ΔPIP restores DNA synthesis to dup null mutant embryonic epidermal cells, but S phase is abnormal, and these cells do not progress into mitosis. In contrast, Dup^ΔPIP accumulation during S phase did not adversely affect progression through follicle cell endocycles in the ovary. In this tissue the combination of Dup^ΔPIP expression and a 50% reduction in Geminin gene dose resulted in egg chamber degeneration. We could not detect Dup hyperaccumulation using mutations in the CRL4^Cdt2 components Cul4 and Ddb1, likely because these cause pleiotropic effects that block cell proliferation. These data indicate that PIP box–mediated destruction of Dup is necessary for the cell division cycle and suggest that Geminin inhibition can restrain Dup^ΔPIP activity in some endocycling cell types.     

Protective efficiency of dendrosomes as novel nano-sized adjuvants for DNA vaccination against birch pollen allergy

We evaluated the use of a novel gene porter (Den123--a nontoxic self-assembled dendritic spheroidal nanoparticle made of biodegradable monomers), aiming to enhance and improve the desired immune response in protection from allergy. Footpad DNA immunization in Balb/c mice was done three times using the Bet v 1a gene with or without Den123 with 2-week intervals followed by sensitization with rBetv1 (5 microg) in alum twice in a weekly interval. Different doses of pCMV-Betv1 were used (10 microg and 100 microg). The protective role of different formulations was evaluated by measuring the IgG1, IgG2a and IgE antibody production, cytokine release of isolated splenocytes and beta-hexosaminidase release from the RBL cells. Higher and increasing ratios of IgG2a/IgG1 were seen in mice which received plasmids in combination with Den123. Den123 and DNA vaccine synergistically enhanced the Interferon gamma released from splenocytes. In the presence of Den123, IgE inhibition was independent of the dose and type of the injected DNA. All DNA-pre-immunized mice demonstrated low basophil degranulation. It is therefore concluded that administration of the DNA entrapped in Den123 nanoparticles results in sustained release of plasmids, Th1/Th2 balanced immune response with promising IgE inhibition. Also higher amounts of DNA contributed to stronger Th1 response.     

RTTN Mutations Link Primary Cilia Function to Organization of the Human Cerebral Cortex

Polymicrogyria is a malformation of the developing cerebral cortex caused by abnormal organization and characterized by many small gyri and fusion of the outer molecular layer. We have identified autosomal-recessive mutations in RTTN, encoding Rotatin, in individuals with bilateral diffuse polymicrogyria from two separate families. Rotatin determines early embryonic axial rotation, as well as anteroposterior and dorsoventral patterning in the mouse. Human Rotatin has recently been identified as a centrosome-associated protein. The Drosophila melanogaster homolog of Rotatin, Ana3, is needed for structural integrity of centrioles and basal bodies and maintenance of sensory neurons. We show that Rotatin colocalizes with the basal bodies at the primary cilium. Cultured fibroblasts from affected individuals have structural abnormalities of the cilia and exhibit downregulation of BMP4, WNT5A, and WNT2B, which are key regulators of cortical patterning and are expressed at the cortical hem, the cortex-organizing center that gives rise to Cajal-Retzius (CR) neurons. Interestingly, we have shown that in mouse embryos, Rotatin colocalizes with CR neurons at the subpial marginal zone. Knockdown experiments in human fibroblasts and neural stem cells confirm a role for RTTN in cilia structure and function. RTTN mutations therefore link aberrant ciliary function to abnormal development and organization of the cortex in human individuals.     

Physicochemical and Rheological Characterization of Gum Tragacanth Exudates from Six Species of Iranian <Emphasis Type="Italic">Astragalus</Emphasis>

The flow behavior of six species of Iranian gum tragacanth dispersions was investigated at different temperatures and ionic strengths, within a concentration range (0.05–1.5% w/w) using a controlled shear rate rheometer. The steady shear measurements showed that all of the gum dispersions had shear-thinning natures. The power law model was used to describe the rheological properties of dispersions and Arrhenius model was used to evaluate the temperature effect. Composition analysis, surface tension measurement, particle size analysis, and color measurement of all the species were also carried out. The results indicated that the six species of gum tragacanth being studied in this paper exhibited significantly different physicochemical properties. Therefore, various species of gum tragacanth can be used instead of different hydrocolloids in a wide range of applications.     

Soils selenium level and esophageal cancer: An ecological study in a high risk area for esophageal cancer

ProjectGolestan province, located in northeast of Iran, has been known as a high risk area for esophageal cancer (EC). This study was conducted to assess the relationship between soils selenium (Se) level and development of EC in this region.ProceduresIn this ecological study, 135 blocks were identified in Golestan province based on geographical altitude and longitude on the map. One soil sample was collected from the center of each block. Then we investigated Se concentration in soil samples by flame atomic absorption spectrometry. Statistical analysis was performed by the Pearson correlation test and Student t-tests. P-values of less than 0.05 were considered as significant.ResultsThe mean±SD of soils Se level in Golestan province was 3.7±1.61 mg/kg. There was a positive correlation between soils Se level and EC rates in this area (P=0.03) (Pearson correlation coefficient=0.19). Soils Se concentration was significantly higher in high (4.13 mg/kg) than in the low (3.39 mg/kg) EC rate areas (P=0.01).ConclusionsWe found high soils Se concentration and a significant positive relationship between soils Se level and EC rate in Golestan province of Iran. So, high soils Se level may play a possible role in developing EC in this area, specifically in Turkmensahra (very high EC rates).     

A computational method for developing hierarchical large deformation viscoelastic models of the contracting heart

In this study, a new computational method for modelling the contracting heart is described. Using this method, the cardiac wall is constructed from basic, repeating contractile units that represent individual myocardial units and collagen, each with its own set of parameters, including orientation, passive and active behaviour and stimulation propagation. The method allows individual control of each structural unit (e.g. at the level of a single myocardial unit). Feasibility of modelling dynamic heart contraction using this method is demonstrated using 2D cross-sections and simplified 3D geometries. Effects of non-contractile scar and myopathic tissue were also tested in these geometrical configurations. Results from the 2D and 3D simulations were, overall, in agreement with well-established physiological data. The present method holds promise for modelling complex heart pathologies, abnormal mechanical properties (e.g. myocardial infarcts) and electrical conduction properties (branch blocks), and their spatial distributions across the myocardial tissues.     

Evaluation of DNA/DNA and prime-boost vaccination using LPG3 against Leishmania major infection in susceptible BALB/c mice and its antigenic properties in human leishmaniasis

One of the main issues in vaccine development is implementation of new adjuvants to improve the antigen presentation and eliciting the protective immune response. Heat shock protein (HSP) molecules are known as natural adjuvants. They can stimulate the innate and adaptive immune response against infectious diseases and cancer. Lipophosphoglycan 3 (LPG3), the Leishmania homologous with GRP94 (glucose regulated protein 94), a member of HSP90 family, is involved in assembly of LPG as the most abundant macromolecule on the surface of Leishmania promastigotes. In the present study as a primary step, we tested LPG3 as a vaccine candidate in two regimens, DNA/DNA and prime-boost (DNA/Protein), against Leishmania major infection in BALB/c mice model. Our results showed that LPG3 and its fragment (rNT-LPG3) are highly immunogenic in BALB/c mice and can stimulate the production of both IgG1 and IgG2a. In prime-boost immunization strategy, the level of antibody response was higher compared with DNA/DNA immunization. The levels of IFN-γ in the supernatant of splenocytes from mice immunized with DNA/DNA and prime-boost regimens were significantly higher when compared to control groups. In fact, immunization with prime-boost vaccination has higher ratio of IFN-γ/IL-5, suggesting a shift towards a Th1 response.In addition, sera reactivity against LPG3 in visceral leishmaniasis (VL) patients was significantly higher in comparison with cutaneous leishmaniasis (CL) patients. Therefore, we recommend further investigations on the usage of LPG3 co-delivery with candidate antigens for vaccine development against leishmaniasis.