Reprogramming of the non-coding transcriptome during brain development

A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs

Nano Positioning Control Using Magnetostrictive Actuators

The focus of this thesis is on the development of control systems for nano- positioning actuators using magnetostrictive materials. Magnetostrictive materials have large strokes and fast responses. However, they are less commonly used than other smart materials such as piezoceramics due to their highly nonlinear and hysteretic behaviour. It is necessary to arrive at an accurate model which can predict the material response at any magnetic field and load condition. Furthermore, due to the nonlinearity of the material, a closed-loop feedback system with a stabilizing controller is needed. Different hysteresis models for magnetostrictive materials are implemented and compared. Since load-dependence is one of the main features of hysteresis for magnetostrictive materials, load-dependent models are studied. An existing load- dependent model is implemented and compared with a new load-dependent hysteresis model which is developed by energy considerations. Passivity of the magnetostrictive system was shown using a physical argument. The results are used to develop a stabilizing controller. Using the properties of the Preisach model, an alternative approach for controller design is proposed. Tracking properties and stability of the controllers were shown. An experimental setup has been developed for data collection and model and controller evaluation

Estrogen receptor-1 is a key regulator of HIV-1 latency that imparts gender-specific restrictions on the latent reservoir.

Unbiased shRNA library screens revealed that the estrogen receptor-1 (ESR-1) is a key factor regulating HIV-1 latency. In both Jurkat T cells and a Th17 primary cell model for HIV-1 latency, selective estrogen receptor modulators (SERMs, i.e., fulvestrant, raloxifene, and tamoxifen) are weak proviral activators and sensitize cells to latency-reversing agents (LRAs) including low doses of TNF-α (an NF-κB inducer), the histone deacetylase inhibitor vorinostat (soruberoylanilide hydroxamic acid, SAHA), and IL-15. To probe the physiologic relevance of these observations, leukapheresis samples from a cohort of 12 well-matched reproductive-age women and men on fully suppressive antiretroviral therapy were evaluated by an assay measuring the production of spliced envelope (env) mRNA (the EDITS assay) by next-generation sequencing. The cells were activated by T cell receptor (TCR) stimulation, IL-15, or SAHA in the presence of either β-estradiol or an SERM. β-Estradiol potently inhibited TCR activation of HIV-1 transcription, while SERMs enhanced the activity of most LRAs. Although both sexes responded to SERMs and β-estradiol, females showed much higher levels of inhibition in response to the hormone and higher reactivity in response to ESR-1 modulators than males. Importantly, the total inducible RNA reservoir, as measured by the EDITS assay, was significantly smaller in the women than in the men. We conclude that concurrent exposure to estrogen is likely to limit the efficacy of viral emergence from latency and that ESR-1 is a pharmacologically attractive target that can be exploited in the design of therapeutic strategies for latency reversal

Contrast and spatial frequency modulation for diagnosis of amblyopia: An electrophysiological approach

Purpose: To evaluate the diagnostic value of visual evoked potentials (VEPs) and to find out which test setting has the most sensitivity and specificity for amblyopia diagnosis. Methods: Thirty-three adult anisometropic amblyopes were intended in this study and were tested for visual evoked potentials with different stimulus conditions including three spatial frequencies 1, 2, and 4-cycles-per-degree (cpd) at four contrast levels (100, 50, 25, and 5%). We also tested psychophysical contrast sensitivity and compared the results with electrophysiological ones. We plotted Receiver Operating Characteristic (ROC) curve for each VEP recording and psychophysical contrast sensitivity to evaluate the area under the curve, sensitivity, specificity, and cut-point value of each test stimulus for detecting amblyopic eyes. Results: Thirty-three amblyopic and 33 non-amblyopic eyes were examined for psychophysical contrast sensitivity and VEPs. Area under the ROC curve (AURC) findings showed that VEP with different stimulus settings can significantly detect amblyopic eyes, as well as psychophysical contrast sensitivity test. We found that P100 amplitudes had the largest AURC in response to stimuli of 2-cpd spatial frequency at 50 (P < 0.001) and 25% (P < 0.001) contrast levels, respectively. Cut-off amplitudes for these stimuli were 8.65 and 4.50 μV, which had a sensitivity of 0.758 and 0.697 and a specificity of 0.788 and 0.848, respectively. The sensitivity and specificity of VEP P100 amplitude in response to the stimuli with 2 cpd spatial frequency and 50 and 25% contrast were greater than the findings obtained from psychophysical contrast sensitivity test. Conclusion: According to our findings, assessment of VEP amplitudes in response to stimuli of 2-cpd spatial frequency at 50 and 25% contrast levels can best detect amblyopia with highest sensitivity and specificity and thus, are the protocols of choice for detection of amblyopic eyes. © 2018 Iranian Society of Ophthalmolog

The distribution of near point of convergence in an Iranian rural population: A population-based cross-sectional study

Objective: To determine the distribution of near point of convergence (NPC) according to age, sex, and refractive error in a rural population above 1 year of age in 2015. Methods: In this population-based cross-sectional study, multistage cluster sampling was applied to randomly select two underserved areas from the north and southwest of Iran and all individuals above 1 year living in these areas were invited to participate in the study. All participants underwent ocular examinations including visual acuity measurement, refraction, binocular vision testing including cover test and measurement of NPC, and slit lamp biomicroscopy. Results: Of 3851 who were invited, 3314 participated in the study (response rate: 86.5). The NPC was 8.42 ± 2.94 cm in the whole population, 8.59 ± 3.07 cm in men, and 8.30 ± 2.84 cm in women. Subjects above 70 years of age had the most remote NPC (mean: 10.44 ± 3.07 cm). The mean NPC was 7.79 ± 2.93, 8.83 ± 2.72, and 9.63 ± 2.70 cm in emmetropic, myopic, and hyperopic participants, respectively. According to the results of a multiple linear regression model, NPC had a positive correlation with age (b: 0.058, p < 0.001), male sex (b: 0.336, p: 0.005), and hyperopia (b: 0.044, p: 0.011). Among the evaluated variables, age had the greatest effect on NPC (Standardized coefficient: 0.402). Conclusion: The distribution of NPC in the Iranian population is different from other populations. Since NPC is influenced by age more than any other variable and presented normal values according to age in this study, the results can be used to interpret clinical measurements for diagnosis and treatment purposes. © 2019 The Author

Overlapping Antisense Transcription in the Human Genome

Accumulating evidence indicates an important role for non-coding RNA molecules in eukaryotic cell regulation. A small number of coding and non-coding overlapping antisense transcripts (OATs) in eukaryotes have been reported, some of which regulate expression of the corresponding sense transcript. The prevalence of this phenomenon is unknown, but there may be an enrichment of such transcripts at imprinted gene loci. Taking a bioinformatics approach, we systematically searched a human mRNA database (RefSeq) for complementary regions that might facilitate pairing with other transcripts. We report 56 pairs of overlapping transcripts, in which each member of the pair is transcribed from the same locus. This allows us to make an estimate of 1000 for the minimum number of such transcript pairs in the entire human genome. This is a surprisingly large number of overlapping gene pairs and, clearly, some of the overlaps may not be functionally significant. Nonetheless, this may indicate an important general role for overlapping antisense control in gene regulation. EST databases were also investigated in order to address the prevalence of cases of imprinted genes with associated non-coding overlapping, antisense transcripts. However, EST databases were found to be completely inappropriate for this purpose

Group II intron in Bacillus cereus has an unusual 3′ extension and splices 56 nucleotides downstream of the predicted site

All group II introns known to date fold into six functional domains. However, we recently identified an intron in Bacillus cereus ATCC 10987, B.c.I4, that splices 56 nt downstream of the expected 3′ splice site in vivo (Tourasse et al. 2005, J. Bacteriol., 187, 5437–5451). In this study, we confirmed by ribonuclease protection assay that the 56-bp segment is part of the intron RNA molecule, and computational prediction suggests that it might form a stable stem-loop structure downstream of domain VI. The splicing of B.c.I4 was further investigated both in vivo and in vitro. Lariat formation proceeded primarily by branching at the ordinary bulged adenosine in domain VI without affecting the fidelity of splicing. In addition, the splicing efficiency of the wild-type intron was better than that of a mutant construct deleted of the 56-bp 3′ extension. These results indicate that the intron has apparently adapted to the extra segment, possibly through conformational adjustments. The extraordinary group II intron B.c.I4 harboring an unprecedented extra 3′ segment constitutes a dramatic example of the flexibility and adaptability of group II introns

Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components

Appropriate expression of most eukaryotic genes requires the removal of introns from their pre–messenger RNAs (pre-mRNAs), a process catalyzed by the spliceosome. In higher eukaryotes a large family of auxiliary factors known as SR proteins can improve the splicing efficiency of transcripts containing suboptimal splice sites by interacting with distinct sequences present in those pre-mRNAs. The yeast Saccharomyces cerevisiae lacks functional equivalents of most of these factors; thus, it has been unclear whether the spliceosome could effectively distinguish among transcripts. To address this question, we have used a microarray-based approach to examine the effects of mutations in 18 highly conserved core components of the spliceosomal machinery. The kinetic profiles reveal clear differences in the splicing defects of particular pre-mRNA substrates. Most notably, the behaviors of ribosomal protein gene transcripts are generally distinct from other intron-containing transcripts in response to several spliceosomal mutations. However, dramatically different behaviors can be seen for some pairs of transcripts encoding ribosomal protein gene paralogs, suggesting that the spliceosome can readily distinguish between otherwise highly similar pre-mRNAs. The ability of the spliceosome to distinguish among its different substrates may therefore offer an important opportunity for yeast to regulate gene expression in a transcript-dependent fashion. Given the high level of conservation of core spliceosomal components across eukaryotes, we expect that these results will significantly impact our understanding of how regulated splicing is controlled in higher eukaryotes as well