Jerusalem

Mourad, Suleiman A.; Mayer, Tamar

doi:10.4324/9780203929773

Cited by 17 publications

(4 citation statements)

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“…Chloroplast microsatellite regions shared in both F. crenata and F. engleriana were searched for in an alignment of the two full chloroplast genomes (constructed by MAFFT v7.308 (Katoh et al, 2002) under default settings) using Phobos Tandem Repeat Finder (Mayer, 2008) implemented in Geneious v9.0.5. Microsatellite in either of the sequences with a repeat unit length of 1–2 bp were searched for using a minimum length of 10 bp while those with a repeat length of 3–6 bp were selected if they displayed three or more repeats.…”

Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

Worth

Liu

Wei

et al. 2019

PeerJ

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This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

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Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

Worth

Liu

Wei

et al. 2019

PeerJ

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“…We used Phobos (Mayer, 2008) to identify potential tandem repeats among all CRISPR candidates we detected. Phobos gives each candidate a score for being a tandem repeat, and we used the default threshold score of ≥10 for tandem repeat determination.…”

Section: Methodsmentioning

confidence: 99%

“…Repeats, spacers, and whole CRISPR arrays need to be checked to exclude potential tandem repeats that are unlikely to be true CRISPR arrays ( Skennerton, Imelfort & Tyson, 2013 ). We used Phobos ( Mayer, 2008 ) to identify potential tandem repeats among all CRISPR candidates we detected. Phobos gives each candidate a score for being a tandem repeat, and we used the default threshold score of ≥10 for tandem repeat determination.…”

Section: Methodsmentioning

confidence: 99%

CRF: detection of CRISPR arrays using random forest

Wang

Liang

2017

PeerJ

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CRISPRs (clustered regularly interspaced short palindromic repeats) are particular repeat sequences found in wide range of bacteria and archaea genomes. Several tools are available for detecting CRISPR arrays in the genomes of both domains. Here we developed a new web-based CRISPR detection tool named CRF (CRISPR Finder by Random Forest). Different from other CRISPR detection tools, a random forest classifier was used in CRF to filter out invalid CRISPR arrays from all putative candidates and accordingly enhanced detection accuracy. In CRF, particularly, triplet elements that combine both sequence content and structure information were extracted from CRISPR repeats for classifier training. The classifier achieved high accuracy and sensitivity. Moreover, CRF offers a highly interactive web interface for robust data visualization that is not available among other CRISPR detection tools. After detection, the query sequence, CRISPR array architecture, and the sequences and secondary structures of CRISPR repeats and spacers can be visualized for visual examination and validation. CRF is freely available at http://bioinfolab.miamioh.edu/crf/home.php.

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“…Moreover, in East Jerusalem, first Jordanian, and then increasingly Palestinian institutions became active players in providing the local Palestinian population with services that the Israeli government and municipality failed to or could not deliver. 49 Among the main challenges to the theoretical concept of sovereignty was the situation over Temple Mount/Haram-Al-Sharif. In many ways, the status-quo arrangement established after the 1967 war marked a contradiction and deviation from the Israeli conception of sovereignty described above.…”

Section: Sovereignty In Jerusalem As a Destabilized Conceptmentioning

confidence: 99%

The state of concept: A new analytical tool for political research

Kibrik¹

2021

International Relations

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This paper proposes a typology of four possible states of concepts: unquestioned, contested, essentially contested, and destabilized. The typology serves as a frame of reference and as an analytical tool for IR researchers who wish to study concepts and conceptualizing processes as a way of understanding politics. It argues that, within a context, every concept is in one out of four possible states. The typology rests on the relationship between experiences, perceptions, and concepts, aiming to rectify the lacuna of minimal attention to the experiences of many IR works which mainly focus on the inter-subjective sphere and actor-structure tensions. Thus, using the example of sovereignty in Jerusalem during the Israeli-Palestinians negotiations (1993–2001), a new state of concept, the destabilized state, is introduced.

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Jerusalem

Cited by 17 publications

References 0 publications

The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

CRF: detection of CRISPR arrays using random forest

The state of concept: A new analytical tool for political research

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