Identification of Hepta- and Octo-Uridine stretches as sole signals for programmed +1 and −1 ribosomal frameshifting during translation of SARS-CoV ORF 3a variants

Programmed frameshifting is one of the translational recoding mechanisms that read the genetic code in alternative ways. This process is generally programmed by signals at defined locations in a specific mRNA. In this study, we report the identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and −1 ribosomal frameshifting during translation of severe acute respiratory syndrome coronavirus (SARS-CoV) ORF 3a variants. SARS-CoV ORF 3a encodes a minor structural protein of 274 amino acids. Over the course of cloning and expression of the gene, a mixed population of clones with six, seven, eight and nine T stretches located 14 nt downstream of the initiation codon was found. In vitro and in vivo expression of clones with six, seven and eight Ts, respectively, showed the detection of the full-length 3a protein. Mutagenesis studies led to the identification of the hepta- and octo-uridine stretches as slippery sequences for efficient frameshifting. Interestingly, no stimulatory elements were found in the sequences upstream or downstream of the slippage site. When the hepta- and octo-uridine stretches were used to replace the original slippery sequence of the SARS-CoV ORF 1a and 1b, efficient frameshift events were observed. Furthermore, the efficiencies of frameshifting mediated by the hepta- and octo-uridine stretches were not affected by mutations introduced into a downstream stem–loop structure that totally abolish the frameshift event mediated by the original slippery sequence of ORF 1a and 1b. Taken together, this study identifies the hepta- and octo-uridine stretches that function as sole elements for efficient +1 and −1 ribosomal frameshift events

Observation of gain-pinned dissipative solitons in a microcavity laser

This work was supported by the National Science Center in Poland, by Grant Nos. 2016/23/N/ST3/01350 and 2018/30/E/ST7/00648, and by the Polish National Agency for Academic Exchange. The Würzburg group gratefully acknowledges support by the State of Bavaria. The work at the Australian National University was supported by the Australian Research Council.We demonstrate an experimental approach for creating spatially localized states in a semiconductor microcavity laser. In particular, we shape the spatial gain profile of a quasi-one-dimensional microcavity laser with a nonresonant, pulsed optical pump to create spatially localized structures, known as gain-pinned dissipative solitons, that exist due to the balance of gain and nonlinear losses. We directly probe the ultrafast formation dynamics and decay of these localized structures, showing that they are created on a picosecond timescale, orders of magnitude faster than laser cavity solitons. All of the experimentally observed features and dynamics are reconstructed by numerical modeling using a complex Ginzburg-Landau model, which explicitly takes into account the carrier density dynamics in the semiconductor.Publisher PDFPeer reviewe

Low energy and dynamical properties of a single hole in the t-Jz model

We review in details a recently proposed technique to extract information about dynamical correlation functions of many-body hamiltonians with a few Lanczos iterations and without the limitation of finite size. We apply this technique to understand the low energy properties and the dynamical spectral weight of a simple model describing the motion of a single hole in a quantum antiferromagnet: the $t-J_z$ model in two spatial dimension and for a double chain lattice. The simplicity of the model allows us a well controlled numerical solution, especially for the two chain case. Contrary to previous approximations we have found that the single hole ground state in the infinite system is continuously connected with the Nagaoka fully polarized state for $J_z \to 0$. Analogously we have obtained an accurate determination of the dynamical spectral weight relevant for photoemission experiments. For $J_z=0$ an argument is given that the spectral weight vanishes at the Nagaoka energy faster than any power law, as supported also by a clear numerical evidence. It is also shown that spin charge decoupling is an exact property for a single hole in the Bethe lattice but does not apply to the more realistic lattices where the hole can describe closed loop paths.Comment: RevTex 3.0, 40 pages + 16 Figures in one file self-extracting, to appear in Phys. Rev

Development of high-speed directly-modulated DFB and DBR lasers with surface gratings

The conventional distributed feedback and distributed Bragg reflector edge-emitting lasers employ buried gratings, which require two or more epitaxial growth steps. By using lateral corrugations of the ridge-waveguide as surface gratings the epitaxial overgrowth is avoided, reducing the fabrication complexity, increasing the yield and reducing the fabrication cost. The surface gratings are applicable to different materials, including Al-containing ones and can be easily integrated in complex device structures and photonic circuits. Single-contact and multiple contact edge-emitting lasers with laterally-corrugated ridge waveguide gratings have been developed both on GaAs and InP substrates with the aim to exploit the photon-photon resonance in order to extend their direct modulation bandwidth. The paper reports on the characteristics of such surface-grating-based lasers emitting both at 1.3 and 1.55 μm and presents the photon-photon resonance extended small-signal modulation bandwidth (> 20 GHz) achieved with a 1.6 mm long single-contact device under direct modulation. Similarly structured devices, with shorter cavity lengths are expected to exceed 40 GHz smallsignal modulation bandwidth under direct modulatio

Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis

Background: Fragile X syndrome and tuberous sclerosis are genetic syndromes that both have a high rate of comorbidity with autism spectrum disorder (ASD). Several lines of evidence suggest that these two monogenic disorders may converge at a molecular level through the dysfunction of activity-dependent synaptic plasticity. Methods: To explore the characteristics of transcriptomic changes in these monogenic disorders, we profiled genome-wide gene expression levels in cerebellum and blood from murine models of fragile X syndrome and tuberous sclerosis. Results: Differentially expressed genes and enriched pathways were distinct for the two murine models examined, with the exception of immune response-related pathways. In the cerebellum of the Fmr1 knockout (Fmr1-KO) model, the neuroactive ligand receptor interaction pathway and gene sets associated with synaptic plasticity such as long-term potentiation, gap junction, and axon guidance were the most significantly perturbed pathways. The phosphatidylinositol signaling pathway was significantly dysregulated in both cerebellum and blood of Fmr1-KO mice. In Tsc2 heterozygous (+/−) mice, immune system-related pathways, genes encoding ribosomal proteins, and glycolipid metabolism pathways were significantly changed in both tissues. Conclusions: Our data suggest that distinct molecular pathways may be involved in ASD with known but different genetic causes and that blood gene expression profiles of Fmr1-KO and Tsc2+/− mice mirror some, but not all, of the perturbed molecular pathways in the brain

Observation of gain-pinned dissipative solitons in a microcavity laser

We demonstrate an experimental approach for creating spatially localized states in a semiconductor microcavity laser. In particular, we shape the spatial gain profile of a quasi-one-dimensional microcavity laser with a nonresonant, pulsed optical pump to create spatially localized structures, known as gain-pinned dissipative solitons, that exist due to the balance of gain and nonlinear losses. We directly probe the ultrafast formation dynamics and decay of these localized structures, showing that they are created on a picosecond timescale, orders of magnitude faster than laser cavity solitons. All of the experimentally observed features and dynamics are reconstructed by numerical modeling using a complex Ginzburg-Landau model, which explicitly takes into account the carrier density dynamics in the semiconductorThis work was supported by the National Science Center in Poland, by Grant Nos. 2016/23/N/ST3/01350 and 2018/30/E/ST7/00648, and by the Polish National Agency for Academic Exchange. The Würzburg group gratefully acknowledges support by the State of Bavaria. The work at the Australian National University was supported by the Australian Research Council

Patterns of Gene Expression in Western Corn Rootworm (\u3ci\u3eDiabrotica virgifera virgifera\u3c/i\u3e) Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on Next-Generation Sequencing

With Next Generation Sequencing technologies, high-throughput RNA sequencing (RNAseq) was conducted to examine gene expression in neonates of Diabrotica virgifera virgifera (LeConte) (Western Corn Rootworm, WCR) challenged with individual proteins of the binary Bacillus thuringiensis insecticidal proteins, Cry34Ab1 and Cry35Ab1, and the combination of Cry34/Cry35Ab1, which together are active against rootworm larvae. Integrated results of three different statistical comparisons identified 114 and 1300 differentially expressed transcripts (DETs) in the Cry34Ab1 and Cry34/35Ab1 treatment, respectively, as compared to the control. No DETs were identified in the Cry35Ab1 treatment. Putative Bt binding receptors previously identified in other insect species were not identified in DETs in this study. The majority of DETs (75% with Cry34Ab1 and 68.3% with Cry34/35Ab1 treatments) had no significant hits in the NCBI nr database. In addition, 92 DETs were shared between Cry34Ab1 and Cry34/35Ab1 treatments. Further analysis revealed that the most abundant DETs in both Cry34Ab1 and Cry34/35Ab1 treatments were associated with binding and catalytic activity. Results from this study confirmed the nature of these binary toxins against WCR larvae and provide a fundamental profile of expression pattern of genes in response to challenge of the Cry34/35Ab1 toxin, which may provide insight into potential resistance mechanisms

RNAi induced knockdown of a cadherin-like protein (EF531715) does not affect toxicity of Cry34/35Ab1 or Cry3Aa to \u3ci\u3eDiabrotica virgifera virgifera\u3c/i\u3e larvae (Coleoptera: Chrysomelidae)

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is an important maize pest throughout most of the U.S. Corn Belt. Bacillus thuringiensis (Bt) insecticidal proteins including modified Cry3Aa and Cry34/35Ab1 have been expressed in transgenic maize to protect against WCR feeding damage. To date, there is limited information regarding the WCR midgut target sites for these proteins. In this study, we examined whether a cadherin-like gene from Diabrotica virgifera virgifera (DvvCad; Gen-Bank accession # EF531715) associated with WCR larval midgut tissue is necessary for Cry3Aa or Cry34/ 35Ab1 toxicity. Experiments were designed to examine the sensitivity of WCR to trypsin activated Cry3Aa and Cry34/35Ab1 after oral feeding of the DvvCad dsRNA to knockdown gene expression. Quantitative real-time PCR confirmed that DvvCad mRNA transcript levels were reduced in larvae treated with cadherin dsRNA. Relative cadherin expression by immunoblot analysis and nano-liquid chromatography–mass spectrometry (nanoLC-MS) of WCR neonate brush border membrane vesicle (BBMV) preparations exposed to DvvCad dsRNA confirmed reduced cadherin expression when compared to BBMV from untreated larvae. However, the larval mortality and growth inhibition of WCR neonates exposed to cadherin dsRNA for two days followed by feeding exposure to either Cry3Aa or Cry34/35Ab1 for four days was not significantly different to that observed in insects exposed to either Cry3Aa or Cry34/35Ab1 alone. In combination, these results suggest that cadherin is unlikely to be involved in the toxicity of Cry3Aa or Cry34/35Ab1 to WCR

Basic Amino Acid Mutations in the Nuclear Localization Signal of Hibiscus Chlorotic Ringspot Virus p23 Inhibit Virus Long Distance Movement

10.1371/journal.pone.0074000PLoS ONE89-POLN

Characteristics and Predictive Value of Blood Transcriptome Signature in Males with Autism Spectrum Disorders

Autism Spectrum Disorders (ASD) is a spectrum of highly heritable neurodevelopmental disorders in which known mutations contribute to disease risk in 20% of cases. Here, we report the results of the largest blood transcriptome study to date that aims to identify differences in 170 ASD cases and 115 age/sex-matched controls and to evaluate the utility of gene expression profiling as a tool to aid in the diagnosis of ASD. The differentially expressed genes were enriched for the neurotrophin signaling, long-term potentiation/depression, and notch signaling pathways. We developed a 55-gene prediction model, using a cross-validation strategy, on a sample cohort of 66 male ASD cases and 33 age-matched male controls (P1). Subsequently, 104 ASD cases and 82 controls were recruited and used as a validation set (P2). This 55-gene expression signature achieved 68% classification accuracy with the validation cohort (area under the receiver operating characteristic curve (AUC): 0.70 [95% confidence interval [CI]: 0.62–0.77]). Not surprisingly, our prediction model that was built and trained with male samples performed well for males (AUC 0.73, 95% CI 0.65–0.82), but not for female samples (AUC 0.51, 95% CI 0.36–0.67). The 55-gene signature also performed robustly when the prediction model was trained with P2 male samples to classify P1 samples (AUC 0.69, 95% CI 0.58–0.80). Our result suggests that the use of blood expression profiling for ASD detection may be feasible. Further study is required to determine the age at which such a test should be deployed, and what genetic characteristics of ASD can be identified