22 research outputs found
Evolution of X chromosome inactivation in therian mammals
No full textIn therian (eutherian and marsupial) mammals, X gene dosage between XY males and XX females is equalized by transcriptional silencing of one X chromosome in the somatic cells of females; a process called X chromosome inactivation (XCI). There are fundamental differences between the random, stable XCI in eutherians, and the paternal and partial system in marsupials, which can be exploited to dissect the mechanisms and evolution of XCI. A striking molecular difference is the involvement of DNA methylation in eutherian XCI, which seems, from a few previous studies, not to be mirrored by marsupials. I therefore searched for sex-specific DNA methylation of X-borne genes in marsupials using mass array bisulfate sequencing (Chapter 2). I tested methylation differences of six X-borne genes in four different tissues of male and female tammar wallaby and identified sex-specific methylation differences in 5' CpG islands of two genes. However, I observed no correlation between methylation status and inactivation of genes. I conclude that DNA methylation plays no role in maintaining inactivation (at least of the loci I examined) in marsupials. To gain new insights into the mechanisms and evolution of XCI I studied gene transcription at the level of individual nuclei (Chapters 3 and 4). I used RNA in situ hybridization to assess whether one or both alleles of X-borne loci were transcribed in fibroblasts from three marsupial model species (tammar wallaby, Tasmanian devil and South American opossum) and three eutherian species (human, mouse and elephant). In marsupials I observed that different X loci have a characteristic frequency of expression from one or both alleles, indicating that it is the probability of expression (either 1X-active or 2X-active), rather than the rate of transcription that contributes to the partial expression of the paternal allele. I observed no polarity that might reveal an X inactivation centre. Most orthologous genes on the conserved region of the eutherian X (XCR) were completely inactivated. However, genes that escape XCI on the evolutionarily distinct added region of the eutherian X (XAR, autosomal in marsupials) were 1X- or 2X-active in reproducible frequencies, analogous to genes on the marsupial X. I therefore proposed that marsupial XCI, and the evolutionarily distinct XAR of the eutherian X, retain features of an ancient incomplete silencing mechanism, which was progressively stabilized (perhaps by the evolution of XIST) on the eutherian XCR. I then tested the hypothesis that incomplete stochastic monoallelic expression represents an ancient mechanism to control gene expression, which was exapted into genomic imprinting, as well as XCI. Genomic imprinting results in parent-specific monoallelic expression, and involves epigenetic modifications similar to genes on the inactive X. I therefore assessed transcription from nine autosomal-imprinted loci in mouse, and their tammar wallaby orthologues. Surprisingly, I observed biallelic expression of imprinted genes in a proportion of mouse and tammar nuclei. As for genes on the marsupial X and the eutherian XAR (as well as genes on the independently evolved platypus sex chromosomes), transcription appeared to be stochastic
Design beyond the eyes: a web-based tool for designers working with people with visual needs
No full textThe proportion of the global population who are elderly is growing which will lead to more people with physical conditions including vision loss. Every person with visual needs has different lived experiences considering their living condition, vision condition, and how long they have been living with vision loss or no vision.
There is a gap between the needs of adults experiencing vision loss and the addressing of those needs by existing products and services, due to the lack of a deep understanding of their needs and challenges by designers. Designers who are not familiar with working with people with visual needs have to gain a deeper understanding of their lived experiences and their variety of needs to be able to design for them effectively. Designers need tools and techniques that will prevent them from generalizing the experiences and challenges of their user group, which can lead to considering only one solution for everyone without understanding and considering their individual and different needs.
Although the focus of this project is on the communication between designers and people with visual needs, the individuality of each participant as a human being with different characteristics and experiences played an important role in the path of this project. The primary research included several online interviews and co-creation sessions with people with visual needs and those who have daily communication with them to understand their needs and experiences comprehensively. As a result of the experimental phase, the author realized that there is a need for improving the interaction between designers and individuals with visual needs which would result in a deeper understanding of the real needs of the users to be considered in the design process.
To meet this goal, journey maps (explained below) were found to be the most effective tools that would give the opportunity to the participants to share their experiences safely, openly, and in detail. Therefore, a web-based tool was created for use by designers who are new to the area of visual needs. It provides them with the required information about this area, as well as guidelines for how to proceed with the design process to produce flexible, adaptable, and accessible journey maps that would give space to everyone to share their personal journey.
The components of this tool help designers in the process of creating journey maps with participants with low or no vision. First, designers get familiar with the common definitions that they need to know before starting the interaction with participants including the kinds and causes of vision loss, and existing assistive technologies. Then, they receive guidelines about how to identify their user group by asking the right questions, as well as guidelines for conducting the interviews which would lead to creating the journey maps. The guidelines for creating the visual and non-visual journey maps provide the designers with the characteristics of the maps and how to make them accessible for the participants considering their vision level and their accessibility to technology.Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-01-12 without embargo termsThe student, Shafagh Hadinezhad, accepted the attached license on 2021-07-20 at 13:03.The student, Shafagh Hadinezhad, submitted this Thesis for approval on 2021-07-20 at 13:05.This Thesis was approved for publication on 2021-07-22 at 16:12.DSpace SAF Submission Ingestion Package generated from Vireo submission #17016 on 2022-01-12 at 12:46:18Made available in DSpace on 2022-01-12T21:46:56Z (GMT). No. of bitstreams: 2
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Previous issue date: 2021-07-2
Marsupial Genetics Reveals Insights into Evolution of Mammalian X Chromosome Inactivation
No full textX chromosome inactivation (X-inactivation; XCI) in mammals equalizes X gene dosage between XX females and XY males. It is the prime example of epigenetic repression on a grand scale. This regulatory process differentially treats homologous chromosomes within the same nucleus to ensure that only a single X chromosome remains active in a diploid female cell. The best-studied models of X-inactivation, humans and mice, represent only one of four clades of placental (eutherian) mammals. Comparisons of dosage compensation mechanisms in distantly related eutherian mammals, marsupial and monotreme mammals, and even birds, will offer entirely new insights to the mechanisms and evolution of dosage compensation. In order to reconstruct what dosage compensation mechanisms might have been functioning in the mammalian ancestor, we highlight the molecular similarities and differences between X-inactivation in marsupials and eutherians, and compare them with the partial dosage compensation system observed in monotreme mammals, which appears more similar to bird dosage compensation. We draw parallels between these mechanisms, which may well have evolved independently by drawing from a common epigenetic “toolbox”, and therefore utilize similar molecular mechanisms to down-regulate gene expression
A comparison between the structure of Hamidi’s Maqamat and Sa’di’s Golestan
No full textAbstract
Maqamat are successive stories in which the hero is the same in all of them. The hero does strange things or in other words stunts and in the end disappears and no one knows his conclusion and again in another story appears in a new character. Maqame can be considered as the highest grade of Picaresque stories that was customary in Spain in the sixtheenth century. Picaresque derived from the Spanish word Picaro which means janus-faced, sly and cunning and Picaresque was the attribute for romances that proceed to Picaros’ actions.
The main Maqame in Farsi, is Hamidi’s Maqamat composed by judge Hamid od-Din Balkhi (d. 559 AH) who was chief justice of Balkh that wrote it in (551 AH) following Maqamat of Badi’ oz-Zaman Hamedani and Hariri.
In discussing about structure of the story, elements such as subject, theme, characterization, plot, point of view, setting, language, time and place are considered as main topics.
Hamidi’s Maqamat imitating of Arabic Maqamat, in most cases has used Arabic words and compounds and did not welcome to Persian style statements as much. That is the reason it is full of complex and difficult words and idioms. Saadi's profound knowledge of Persian-language capabilities, understanding people's alive and vibrant slang and proficiency in fusion power of Persian-language, more use of prefix and simple verbs, utilization of metonyms, observance the brevity and briefness, abstaining from difficult words, avoiding of hyperbaton and formality, accuracy in selecting the words, all are effective factors at his innovative work which is Golestan.
In some of Golestan stories, Sa’di himself is the hero and the main character. In some he plays an important role and in some others plays the minor role or is only a spectator and event viewer. The characters are static in Hamidi’s Maqamat. That means at the end of the story, the characters are the same they have been at the beginning. Story events have low impact on them and do not change them. The space and scene of the story in Maqamat, because Balkhi has tendency to periphrasis description, transmits to reader with more details while Saadi's descriptions are very brief and he quickly passes through the atmosphere and the scene of the story.
Plot of Hamidi’s Maqamat in comparison with Golestan, is more consistent and somewhat follows the logic. But the plot of lots of Golestan stories is not more than a joke or sketch, and those stories that involve advice has been written without any sketch.
Most of the Maqamat stories narrate from the exterior view perspective and the narrator as omniscient leads the story characters. But in Golestan the view perspective is fisrt person and the author is a storyteller.
From the characterization perspective, story characters in both Magahamat and Golestan do not change. In lots of Golestan stories, the omniscient narrator (author) or third person narrator and other characters have tangible presence. Sometimes Sa’di himself is the hero of the story whole in Hamidi’s Maqamat the main character as the hero of the story even does not have a specified name.
Intense interest of Hamid od-Din Balkhi in word prolongation to describe time and space has caused the time and space factors are not interesting and clear to the reader. Sometimes also in Golestan the time and space factors are vague, concise and unknown. In Hamidi’s Maqamat all of the stories bring up from the view of unlimited omniscient, but Ghazi Balkhi as says ''narrated me my friend who …'' yet tries to express events as if he had been the looker on and supervisor himself by being in one of the story heroes sho
A comparison between the structure of Hamidiâs Maqamat and Saâdiâs Golestan
No full textAbstract Maqamat are successive stories in which the hero is the same in all of them. The hero does strange things or in other words stunts and in the end disappears and no one knows his conclusion and again in another story appears in a new character. Maqame can be considered as the highest grade of Picaresque stories that was customary in Spain in the sixtheenth century. Picaresque derived from the Spanish word Picaro which means janus-faced, sly and cunning and Picaresque was the attribute for romances that proceed to Picarosâ actions.  The main Maqame in Farsi, is Hamidiâs Maqamat composed by judge Hamid od-Din Balkhi (d. 559 AH) who was chief justice of Balkh that wrote it in (551 AH) following Maqamat of Badiâ oz-Zaman Hamedani and Hariri. In discussing about structure of the story, elements such as subject, theme, characterization, plot, point of view, setting, language, time and place are considered as main topics.   Hamidiâs Maqamat imitating of Arabic Maqamat, in most cases has used Arabic words and compounds and did not welcome to Persian style statements as much. That is the reason it is full of complex and difficult words and idioms. Saadi's profound knowledge of Persian-language capabilities, understanding people's alive and vibrant slang and proficiency in fusion power of Persian-language, more use of prefix and simple verbs, utilization of metonyms, observance the brevity and briefness, abstaining from difficult words, avoiding of hyperbaton and formality, accuracy in selecting the words, all are effective factors at his innovative work which is Golestan.  In some of Golestan stories, Saâdi himself is the hero and the main character. In some he plays an important role and in some others plays the minor role or is only a spectator and event viewer. The characters are static in Hamidiâs Maqamat. That means at the end of the story, the characters are the same they have been at the beginning. Story events have low impact on them and do not change them. The space and scene of the story in Maqamat, because Balkhi has tendency to periphrasis description, transmits to reader with more details while Saadi's descriptions are very brief and he quickly passes through the atmosphere and the scene of the story.   Plot of Hamidiâs Maqamat in comparison with Golestan, is more consistent and somewhat follows the logic. But the plot of lots of Golestan stories is not more than a joke or sketch, and those stories that involve advice has been written without any sketch.   Most of the Maqamat stories narrate from the exterior view perspective and the narrator as omniscient leads the story characters. But in Golestan the view perspective is fisrt person and the author is a storyteller. From the characterization perspective, story characters in both Magahamat and Golestan do not change. In lots of Golestan stories, the omniscient narrator (author) or third person narrator and other characters have tangible presence. Sometimes Saâdi himself is the hero of the story whole in Hamidiâs Maqamat the main character as the hero of the story even does not have a specified name.    Intense interest of Hamid od-Din Balkhi in word prolongation to describe time and space has caused the time and space factors are not interesting and clear to the reader. Sometimes also in Golestan the time and space factors are vague, concise and unknown. In Hamidiâs Maqamat all of the stories bring up from the view of unlimited omniscient, but Ghazi Balkhi as says ''narrated me my friend who â¦'' yet tries to express events as if he had been the looker on and supervisor himself by being in one of the story heroes sho
A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation
No full textSex chromosome dosage compensation in both eutherian and marsupial mammals is achieved by X chromosome inactivation (XCI)—transcriptional repression that silences one of the two X chromosomes in the somatic cells of females. We recently used RNA fluorescent in situ hybridization (FISH) to show, in individual nuclei, that marsupial X inactivation (in the absence of XIST) occurs on a gene-by-gene basis, and that escape from inactivation is stochastic and independent of gene location. In the absence of similar data from fibroblast cell lines of eutherian representatives, a meaningful comparison is lacking. We therefore used RNA-FISH to examine XCI in fibroblast cell lines obtained from three distantly related eutherian model species: African savannah elephant (Loxodonta africana), mouse (Mus musculus) and human (Homo sapiens). We show that, unlike the orthologous marsupial X, inactivation of the X conserved region (XCR) in eutherians generally is complete. Two-colour RNA-FISH on female human, mouse and elephant interphase nuclei showed that XCR loci have monoallelic expression in almost all nuclei. However, we found that many loci located in the evolutionarily distinct recently added region (XAR) displayed reproducible locusspecific frequencies of nuclei with either one or two active X alleles. We propose that marsupial XCI retains features of an ancient incomplete silencing mechanism that was augmented by the evolution of the XIST gene that progressively stabilized the eutherian XCR. In contrast, the recently added region of the eutherian X displays an incomplete inactivation profile similar to that observed on the evolutionarily distinct marsupial X and the independently evolved monotreme X chromosomes
Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic
No full textActivity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic
No full textBACKGROUND:
X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and occurs in the absence of an XIST orthologue.
RESULTS:
We examined expression of X-borne genes using quantitative PCR, revealing a range of dosage compensation for different loci. To assess the frequency of 1X- or 2X-active fibroblasts, we investigated expression of 32 X-borne genes at the cellular level using RNA-FISH. In female fibroblasts, two-color RNA-FISH showed that genes were coordinately expressed from the same X (active X) in nuclei in which both loci were inactivated. However, loci on the other X escape inactivation independently, with each locus showing a characteristic frequency of 1X-active and 2X-active nuclei, equivalent to stochastic escape. We constructed an activity map of the tammar wallaby inactive X chromosome, which identified no relationship between gene location and extent of inactivation, nor any correlation with the presence or absence of a Y-borne paralog.
CONCLUSIONS:
In the tammar wallaby, one X (presumed to be maternal) is expressed in all cells, but genes on the other (paternal) X escape inactivation independently and at characteristic frequencies. The paternal and incomplete X chromosome inactivation in marsupials, with stochastic escape, appears to be quite distinct from the X chromosome inactivation process in eutherians. We find no evidence for a polar spread of inactivation from an X inactivation center.This project was funded by grants to JAMG and PDW from the Australian Research Council
Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic
No full textBackground: X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and occurs in the absence of an XIST orthologue. Results: We examined expression of X-borne genes using quantitative PCR, revealing a range of dosage compensation for different loci. To assess the frequency of 1X- or 2X-active fibroblasts, we investigated expression of 32 X-borne genes at the cellular level using RNA-FISH. In female fibroblasts, two-color RNA-FISH showed that genes were coordinately expressed from the same X (active X) in nuclei in which both loci were inactivated. However, loci on the other X escape inactivation independently, with each locus showing a characteristic frequency of 1X-active and 2X-active nuclei, equivalent to stochastic escape. We constructed an activity map of the tammar wallaby inactive X chromosome, which identified no relationship between gene location and extent of inactivation, nor any correlation with the presence or absence of a Y-borne paralog. Conclusions: In the tammar wallaby, one X (presumed to be maternal) is expressed in all cells, but genes on the other (paternal) X escape inactivation independently and at characteristic frequencies. The paternal and incomplete X chromosome inactivation in marsupials, with stochastic escape, appears to be quite distinct from the X chromosome inactivation process in eutherians. We find no evidence for a polar spread of inactivation from an X inactivation center
Development and characterization of single polymer composites prepared by compression molding of polyamide 6 empty microcapsules and novel woven textile structures
No full textSupplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.mtcomm.2020.100912.In the present study, novel polyamide 6 based woven single polymer composites (WSPC) were developed by
powder-coating of woven textile structures with polyamide 6 empty microcapsules (EMC) and subsequent
compression molding. To synthesize EMC, activated anionic ring-opening polymerization of ε-caprolactam by
solution/precipitation was applied. Stitched plain fabrics that are promising novel class of woven fabrics and two
conventional woven patterns (plain and satin-5 harness) were used as textile reinforcements. The thermal and
mechanical properties of all composites were characterized and related to the reinforcements´ morphology, fiber volume fraction and ply orientation. For better understanding of the bonding state at the matrix-fiber interface, stereo-optical microscopy and SEM image analysis by image processing were performed. The data obtained confirmed the existence of a transcrystalline layer (TCL) in the interface region. The mechanical behavior of the composites was related also to the PA6 polymorph content of the samples and their crystallinity indexes determined by wide-angle X-ray diffraction experiments.All authors gratefully acknowledge the support of the project TSSiPRO-NORTE-01-0145-FEDER-000015 funded by the regional operational program NORTE 2020, under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund. The partial support by FEDER funds through the COMPETE program and by national funds through FCT – Foundation for Science and Technology within the project POCI-01-0145-FEDER-007136is also acknowledged. S. D. Tohidi acknowledges FCT for the financial support through the project SFRH/BD/94759/2013. Moreover, the first author thanks for the financial support of the European Regional Development Fund (ERDF), through the operational program for COMPETE 2020 and
by FCT within the project PTDC/EMEEME/30967/2017 and NORTE 0145-FEDER-030967. Additionally, N. Dencheva is also grateful for the financial support of FCTin the frames of the strategic project UID/CTM/50025/2013 and the personal program-contract CTTI-51/18-IPC
