scholarly journals PATACSDB—the database of polyA translational attenuators in coding sequences

2016 ◽  
Vol 2 ◽  
pp. e45 ◽  
Author(s):  
Malgorzata Habich ◽  
Sergej Djuranovic ◽  
Pawel Szczesny
Keyword(s):  
Gene Dosage ◽  
Interesting Case ◽  
Minimal Length ◽  
Regulatory Mechanisms ◽  
Coding Sequences ◽  
Translation Apparatus ◽  
Dosage Balance ◽  
The Stability ◽  
Eukaryotic Genomes

Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A’s allowing for one mismatched base. The PATACSDB database is accessible at:http://sysbio.ibb.waw.pl/patacsdb. The source code is available athttp://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

scholarly journals PATACSDB - The database of polyA translational attenuators in coding sequences

2015 ◽  
Author(s):  
Malgorzata Habich ◽  
Sergej Djuranovic ◽  
Pawel Szczesny
Keyword(s):  
Gene Dosage ◽  
Interesting Case ◽  
Minimal Length ◽  
Regulatory Mechanisms ◽  
Coding Sequences ◽  
Translation Apparatus ◽  
Recent Addition ◽  
Dosage Balance ◽  
The Stability ◽  
Eukaryotic Genomes

Recent addition to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such they substantially influence the stability of mRNA and amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance, and makes each of these sequences potentially interesting case studies for effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present the PATACSDB, a resource that contain comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accesible at: http://sysbio.ibb.waw.pl/patacsdb. Source code is available for download from GitHub repository at http://github.com/habich/PATACSDB, including the scripts to recreate the database from the scratch on user's own computer.

scholarly journals PATACSDB - The database of polyA translational attenuators in coding sequences

2015 ◽  
Author(s):  
Malgorzata Habich ◽  
Sergej Djuranovic ◽  
Pawel Szczesny
Keyword(s):  
Gene Dosage ◽  
Interesting Case ◽  
Minimal Length ◽  
Regulatory Mechanisms ◽  
Coding Sequences ◽  
Translation Apparatus ◽  
Recent Addition ◽  
Dosage Balance ◽  
The Stability ◽  
Eukaryotic Genomes

Recent addition to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such they substantially influence the stability of mRNA and amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance, and makes each of these sequences potentially interesting case studies for effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present the PATACSDB, a resource that contain comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accesible at: http://sysbio.ibb.waw.pl/patacsdb. Source code is available for download from GitHub repository at http://github.com/habich/PATACSDB, including the scripts to recreate the database from the scratch on user's own computer.

scholarly journals Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos

2021 ◽  
Vol 376 (1833) ◽  
pp. 20200102 ◽  
Author(s):  
Michail Rovatsos ◽  
Tony Gamble ◽  
Stuart V. Nielsen ◽  
Arthur Georges ◽  
Tariq Ezaz ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Gene Dosage ◽  
Regulatory Mechanisms ◽  
Gene Copy ◽  
Male And Female ◽  
Gene Dose ◽  
Female Heterogamety ◽  
Dosage Balance ◽  
Male Heterogamety

Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32–72 Ma, one species in particular, Burton's legless lizard ( Lialis burtonis ), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos

2020 ◽  
Author(s):  
Michail Rovatsos ◽  
Tony Gamble ◽  
Stuart V. Nielsen ◽  
Arthur Georges ◽  
Tariq Ezaz ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Gene Dosage ◽  
Regulatory Mechanisms ◽  
Gene Copy ◽  
Male And Female ◽  
Gene Dose ◽  
Female Heterogamety ◽  
Dosage Balance ◽  
Male Heterogamety

AbstractDifferentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 million years ago, one species in particular, Burton’s legless lizard (Lialis burtonis), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety.

2018 Fiji Election Results: Patterns of Voting by Provinces, Rural-Urban Localities, and by Candidates

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Haruo Nakagawa
Keyword(s):  
Political Parties ◽  
Electoral System ◽  
Interesting Case ◽  
The Political ◽  
Quantitative Analyses ◽  
Election Results

Akin to the previous, 2014 event, with no data on voter ethnicity, no exit polls, and few post-election analyses, the 2018 Fiji election results remain something of a mystery despite the fact that there had been a significant swing in voting in favour of Opposition political parties. There have been several studies about the election results, but most of them have been done without much quantitative analyses. This study examines voting patterns of Fiji’s 2018 election by provinces, and rural-urban localities, as well as by candidates, and also compares the 2018 and 2014 elections by spending a substantial time classifying officially released data by polling stations and individual candidates. Some of the data are then further aggregated according to the political parties to which those candidates belonged. The current electoral system in Fiji is a version of a proportional system, but its use is rare and this study will provide an interesting case study of the Open List Proportional System. At the end of the analyses, this study considers possible reasons for the swing in favour of the Opposition.

Toward a Philosophical Approach of the Hermeneutics of the Qur’an

2006 ◽  
Vol 23 (1) ◽  
pp. 15-34
Author(s):  
Aliaa Ibrahim Dakroury
Keyword(s):  
Modern Technology ◽  
Interesting Case ◽  
Philosophical Approach ◽  
True Meaning ◽  
Flow Of Information ◽  
The Relationship

Although claims questioning whether religious sacred books can be “translated” or not have been heard for quite some time, they have increased with the emergence of globalization and the increasing openness and flow of information due to modern technology. In the context of the relationship between hermeneutics and communication, one could argue that interpreting the Qur’an is an interesting case study for many reasons. Among them is the number of debates and discourses that have been raised both for and against its translation. Another reason, perhaps one of the largest barriers according to some religious Muslim groups, is that the Qur’an is fundamentally revealed and written in Arabic, and, therefore, its true meaning cannot be translated into another language. Certain verses, such as “It is a Qur’an in Arabic, without any crookedness (therein): in order that they may guard against evil” (28:39), have been presented to support this argument.

Management of Optic Neuritis in Ayurveda - A Special Case Report

2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Dr. Harsha S. ◽  
Dr. Mamatha KV.
Keyword(s):  
Optic Nerve ◽  
Optic Neuritis ◽  
Visual Information ◽  
Vision Loss ◽  
Specific Treatment ◽  
Interesting Case ◽  
Treatment Modalities ◽  
Further Development ◽  
Special Case

The optic nerve carries visual information from your eye to your brain. Optic neuritis is when your optic nerve becomes inflamed. Optic neuritis can flare up suddenly from an infection or nerve disease. The inflammation usually causes temporary vision loss that typically happens in only one eye. Those with Optic neuritis sometimes experience pain. As you recover and the inflammation goes away, your vision will likely return. There are no direct references in our classics regarding optic neuritis but can be contemplated as a condition by name Parimlayi Timira. The specific management as such is not cited but a transcendence approach can be done with adopting the treatment which has the ability to pacify the already occurred pathology and prevent the further development of the disease. One such interesting case study on Optic neuritis is elaborated here where in specific treatment modalities (Shodana, Shamana and Kriyakalpas) played role in pacifying the condition.

Science Fiction and Administrative Truths: The Short Story and Novella as Administrative Cases

Public Voices ◽  
2017 ◽  
Vol 2 (3) ◽  
pp. 61
Author(s):  
Nolan J. Argyle ◽  
Lee M. Allen
Keyword(s):  
Science Fiction ◽  
Public Administration ◽  
Short Story ◽  
Interesting Case ◽  
Organizational Complexity ◽  
Professional Career ◽  
Playing Field ◽  
Advantages And Disadvantages ◽  
Hands On

Pre-service and in-service MPA students share a common desire for hands-on, real world instruction related to their professional career goals, leading to a pedagogic discounting of fiction as an appropriate tool for analyzing and "solving" problems. However, several factors weigh heavily in favor of using science fiction short stories and novellas in the MPA classroom setting. These include the need for interesting case scenarios exploring various administrative issues; leveling the playing field between the two types of students by de-emphasizing the use of "contemporary" cases; access to literature that explores the future shock of increasing organizational complexity; and the desirability of Rorschach type materials that facilitate discussion of. values and administrative truths. The discussion proceeds by tracing the development of the case study technique, its advantages and disadvantages in the classroom, addressing the utility of "fiction" as an educational resource, and showing how the science fiction literature has matured to the point where it can be applied in all of the major sub-fields of public administration. Several outstanding examples are detailed, and a thorough bibliography is provided.

Heineken's Acquisition of Asia Pacific Breweries: Accounting for Business Combinations and Changes in Ownership Interests

2017 ◽  
Vol 32 (4) ◽  
pp. 101-127 ◽  
Author(s):  
Pearl Tan ◽  
Chu-Yeong Lim
Keyword(s):  
Market Share ◽  
Joint Venture ◽  
Interesting Case ◽  
Asia Pacific ◽  
Joint Control ◽  
Business Combinations ◽  
Final Offer ◽  
Control Premium ◽  
Joint Venture Partner

ABSTRACT On July 20, 2012, Heineken, a Dutch brewery offered S$5.125 billion (Singapore dollars; approximately US$4.1 billion) to buy Asia Pacific Breweries Ltd (APB; formerly, Malayan Breweries Limited) from its Singapore-based joint venture partner, Fraser and Neave, Limited. (F&N). At that point, Heineken and F&N had joint control over APB through the joint venture vehicle Asia Pacific Investments Pte Ltd (APIPL). Brewery business under the joint arrangement had moved on quite predictably from the time APB was formed in 1931. However, the calm changed to high drama when Thai Beverage, owned by one of Thailand's tycoons, made a bid for F&N and APB. Heineken was quick to respond by aggressively buying shares of APB, leading to a large control premium being paid in the final offer price. The bidding war was largely motivated by the Dutch and Thai beer giants, each wanting to own the iconic Tiger beer brand that was owned by APB and thus take control of APB's strong market share in the fast-growing market of Asia. The Heineken bid for APB presents an interesting case study regarding the motivations for acquisitions, the nature of control, and accounting for acquisitions. The case also presents rich issues in accounting for changes in ownership interests with and without gain of control.

Applications of random graphs

2017 ◽  
Author(s):  
A.C.C. Coolen ◽  
A. Annibale ◽  
E.S. Roberts
Keyword(s):  
Social Networks ◽  
Random Graphs ◽  
Interaction Network ◽  
Power Grids ◽  
Protein Protein Interaction ◽  
Topological Features ◽  
First Case ◽  
The Stability ◽  
Protein Protein Interaction Network

This chapter reviews graph generation techniques in the context of applications. The first case study is power grids, where proposed strategies to prevent blackouts have been tested on tailored random graphs. The second case study is in social networks. Applications of random graphs to social networks are extremely wide ranging – the particular aspect looked at here is modelling the spread of disease on a social network – and how a particular construction based on projecting from a bipartite graph successfully captures some of the clustering observed in real social networks. The third case study is on null models of food webs, discussing the specific constraints relevant to this application, and the topological features which may contribute to the stability of an ecosystem. The final case study is taken from molecular biology, discussing the importance of unbiased graph sampling when considering if motifs are over-represented in a protein–protein interaction network.

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