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Core Eudicots: Dicotyledons V
Published in Donald H. Les, Aquatic Dicotyledons of North America, 2017
Systematics:Justicia is the type genus of tribe Justicieae (Acanthaceae), which is demonstrably monophyletic by phylogenetic analysis of nucleotide sequence and indel data, and by their unusual tricolporate hexapseudocolpate pollen. Tribe Justicieae resolves as the sister clade to tribe Ruellieae (Figure 5.51). However, Justicia is itself problematical taxonomically. Although fewer than a dozen Justicia species have been included in phylogenetic analyses, the preliminary results clearly indicate that the genus is not monophyletic as currently circumscribed, but comprises distinct New World and Old World components (Figure 5.54). Justicia lanceolata (retained here as a species in compliance with the 2013 indicator list) is treated by many authors as a variety of J. ovata. Relationships among the obligate aquatic species have not been clarified. Of the four OBL North American species, only J. americana has been included in phylogenetic analyses; however, never with sufficient representation of taxa to determine even its proximity of relationship to New World vs. Old World species. Further systematic studies of this large and complex genus are needed. The basic chromosome number in Justicia is not readily interpretable, not only because the genus is polyphyletic, but also because of extensive variation in the haploid numbers reported (n = 7, 9, 11–18, 22, 27, 28, 31). The gametic number n = 14 occurs most commonly and x = 7 has been suggested as the base number for the genus. Chromosome numbers are not available for any the OBL North American species.
Genome Editing and Gene Therapies: Complex and Expensive Drugs
Published in Peter Grunwald, Pharmaceutical Biocatalysis, 2020
Finally, the group of Charpentier (Fonfara et al., 2016) reported the detection of a novel mechanism in CRISPR-Cas immunity. The enzyme Cpf1 from Francisella novicida (see also Zetsche et al., 2015, for a first characterization of the Cpf1 enzyme) is a dual nuclease, the first one described up to now, containing a RNase activity unable to cleave DNA and a DNase motif with cleavage activity only toward ds and ss target DNA, both in presence of Mg2+ ions (and Ca2+ ions for DNA cleavage). This CRIPR immunity is the most minimalistic known thus far as it processes pre-crRNA by cleaving it upstream of a hairpin structure within CRISPR repeats to generate intermediate and mature crRNA (Fonfara et al., 2016) which is used to introduce ds breaks in target DNA. The RNA-guided class II CRISPR/Cas system, CRISPR/Cpf1, is different from the CRISPR/Cas9 system in that the PA motif sequence (PAM is T-rich instead of G-rich) frequency in the respective gene is higher, and that the Cpf1 nuclease creates staggered double-strand breaks, which may be of advantage for knock-in applications. Safari et al. (2019) wrote a review dealing with the structural features of Cpf1, the way in which these features affect guide RNA binding as well as DNA targeting, and cleavage. Engineered Cpf1 variants and applications of DNAase deactivated Cpf1 and employment of Cpf1 for genome editing are also discussed. A variety of publications report about engineering of CRISPR RNA for highly efficient genome editing by Cpf1; for instance, Moon et al. (2018; see also literature cited therein) constructed a crRNA containing a repeat sequence, a 20-nt target-complementary sequence, and an uridinylate-rich 3¢-overhang which, due to its significantly improved indel efficiency enabled a highly efficient and specific genome editing by Cpf1. Verwaal et al. (2018) demonstrated the fast and simple applicability of the three Cpf1 orthologues—Acidaminococcus spp. BV3L6 (AsCpf1), Lachnospiraceae bacterium ND2006 (LbCpf1) and Francisella novicida U112 (FnCpf1) for genome editing of Saccharomyces cerevisiae.
Extracting process hierarchies by multi-sequence alignment adaptations
Published in Enterprise Information Systems, 2022
Alternatively, the InDel scoring is handled as the complementary of two edit operations as indicated in Equation 8: insertion and deletion. As in the opportunity cost, confidence-enhanced dynamic cost function assigns a default – confThr value to the InDel and this default value can be exaggerated by insertion and deletion of elements not conforming to business rules. Insertion cost (insCostI(Ii,mk,j,nl) given in Equation 9) compares the as-is business rule with the relative cost of inserting the character from other individual (j,nl) between the current character (Ii,mk) and its successor element (Ii+1k). The potential cost of deletion character Ij,nl from individual I is handled by deletion cost (delCostI(Ij,nk) given in Equation 10).
Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis
Published in Cyber-Physical Systems, 2022
Asim Kumar Mahadani, Shashank Awasthi, Goutam Sanyal, Partha Bhattacharjee, Sanjeev Pippal
This modified Kimura 2 Parameter (Indel-K2P) model enables us to estimate the evolutionary distance in terms of nucleotide substitution along with insertion and deletion (Gap). The derivation of this substitution model is based on the theory of homogeneous Markov process. The genetic distance derived using the modified model is given below:
Genetic variants within the COL5A1 gene are associated with ligament injuries in physically active populations from Australia, South Africa, and Japan
Published in European Journal of Sport Science, 2023
Javier Alvarez-Romero, Mary-Jessica N. Laguette, Kirsten Seale, Macsue Jacques, Sarah Voisin, Danielle Hiam, Julian A. Feller, Oren Tirosh, Eri Miyamoto-Mikami, Hiroshi Kumagai, Naoki Kikuchi, Nobuhiro Kamiya, Noriyuki Fuku, Malcolm Collins, Alison V. September, Nir Eynon
Small-scale independent studies have explored associations between the COL5A1 3’-UTR rs12772 C/T and rs10628678 AGGG/deletion (AGGG/-) indel genetic variants in musculoskeletal soft tissue injuries and exercise-related phenotypes, ranging from recreational participants to elite athletes (Supplementary Table 1).