scholarly journals Identification and Characterization of an Isoform Antifreeze Protein from the Antarctic Marine Diatom, Chaetoceros neogracile and Suggestion of the Core Region

Marine Drugs ◽  
2017 ◽  
Vol 15 (10) ◽  
pp. 318 ◽  
Author(s):  
Minjae Kim ◽  
Yunho Gwak ◽  
Woongsic Jung ◽  
EonSeon Jin
2019 ◽  
Author(s):  
Wei Fang ◽  
Yi Wen ◽  
Xiangyun Wei

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.


2003 ◽  
Vol 52 (3) ◽  
pp. 239-245 ◽  
Author(s):  
Hsing-Yu Hwang ◽  
Chung-Yu Chang ◽  
Lin-Li Chang ◽  
Shui-Feng Chang ◽  
Ya-Hui Chang ◽  
...  

Sixty-three rifampicin-resistant (Rifr) isolates of Mycobacterium tuberculosis from Kaohsiung, Taiwan, were analysed for mutations in the core region (69 bp, codons 511–533) of the rpoB gene. Some 84.1 % (53/63) of the resistant isolates showed mutations in this region, especially in codons 531 (41.5 %), 526 (18.9 %), 516 (15.1 %) and 533 (7.5 %). Five novel alleles of a total of 16 different types of mutations were identified in Rifr isolates. Ten Rifr isolates (15.9 %) exhibited no mutations in the core region of rpoB. Also, they did not show mutations in another 365 bp fragment (codons 99–220) of rpoB. The agar proportion method was used to determine the relationship between the degree of rifampicin resistance and alterations in the core region of rpoB. The results revealed that the mean MIC was 92.38 μg ml−1 for the 53 isolates with a mutation in the core region, whereas the mean MIC of the other 10 isolates without mutations was only 24.8 μg ml−1. This indicates that the isolates with mutations in the core region had higher levels of resistance than those without mutations in this region. IS6110 restriction fragment length polymorphism (RFLP) was used for typing of 55 Rifr M. tuberculosis isolates. Isolates contained two to 19 copies of IS6110, with sizes ranging from 600 to 16 000 bp. The majority (85 %) contained six to 16 copies. No strains lacking IS6110 were found. A total of 54 of 55 RFLP types were defined at the 90 % similarity level. The observation of varied IS6110-associated banding patterns indicates that an outbreak of drug-resistant tuberculosis did not occur in this area.


Polar Biology ◽  
2016 ◽  
Vol 40 (3) ◽  
pp. 649-658 ◽  
Author(s):  
Evelin Troncoso ◽  
Salvador Barahona ◽  
Mario Carrasco ◽  
Pablo Villarreal ◽  
Jennifer Alcaíno ◽  
...  

2019 ◽  
Vol 20 (7) ◽  
pp. 1583 ◽  
Author(s):  
Dàmaris Navío ◽  
Mireia Rosell ◽  
Josu Aguirre ◽  
Xavier de la Cruz ◽  
Juan Fernández-Recio

One of the known potential effects of disease-causing amino acid substitutions in proteins is to modulate protein-protein interactions (PPIs). To interpret such variants at the molecular level and to obtain useful information for prediction purposes, it is important to determine whether they are located at protein-protein interfaces, which are composed of two main regions, core and rim, with different evolutionary conservation and physicochemical properties. Here we have performed a structural, energetics and computational analysis of interactions between proteins hosting mutations related to diseases detected in newborn screening. Interface residues were classified as core or rim, showing that the core residues contribute the most to the binding free energy of the PPI. Disease-causing variants are more likely to occur at the interface core region rather than at the interface rim (p < 0.0001). In contrast, neutral variants are more often found at the interface rim or at the non-interacting surface rather than at the interface core region. We also found that arginine, tryptophan, and tyrosine are over-represented among mutated residues leading to disease. These results can enhance our understanding of disease at molecular level and thus contribute towards personalized medicine by helping clinicians to provide adequate diagnosis and treatments.


2005 ◽  
Vol 62 (1) ◽  
pp. 25-32 ◽  
Author(s):  
David A. Demer ◽  
Stéphane G. Conti

Abstract Antarctic krill, Euphausia superba, comprises the foundation of the foodweb in the Southern Ocean and is the target of a large fishery. Recently, the total abundance of krill in the Scotia Sea was estimated from an international echosounder and net survey (CCAMLR 2000) to be 44.3 million metric tonnes (Mt; CV 11.4%) (Hewitt et al., 2002). The new biomass estimate prompted the Antarctic Treaty's Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) to revise the precautionary catch level for krill in the area from 1.5 to 4 Mt (SC-CAMLR, 2000). These survey results are based on the total echo energy attributed to krill, scaled by the Greene et al. (1991) model of krill acoustical reflectivity or target strength (TS). Presented here is a re-analysis of the CCAMLR 2000 data incorporating recent improvements in the characterization of krill TS. The results indicate that the estimated krill biomass in the Scotia Sea may be as high as 192.4 Mt (CV = 11.7%), or as low as 109.4 Mt (CV = 10.4%), depending solely on the expected distribution of krill orientations. The new Stochastic, Distorted-Wave, Born-Approximation (SDWBA) TS model solved with an empirically estimated distribution of in situ orientations leads to a krill-biomass estimate that is nearly 2.5 times the previous estimate. In consequence, revisions may be warranted of the standard krill TS model, the CCAMLR 2000 biomass estimate, and the associated precautionary catch level for krill in the Scotia Sea.


2010 ◽  
Vol 8 (23) ◽  
pp. 5404 ◽  
Author(s):  
Giuseppina Pieretti ◽  
Sara Carillo ◽  
Barbara Nicolaus ◽  
Annarita Poli ◽  
Rosa Lanzetta ◽  
...  

2001 ◽  
Vol 16 (3) ◽  
pp. 465-499 ◽  
Author(s):  
Erik Jaap Molenaar

AbstractThe Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR Convention) forms the core of the regulatory regime for Southern Ocean fisheries. This article analyses the scope and extent of the Convention and the competence of the bodies established under it while also addressing the role of states and other international intergovernmental organisations with relevant competence. As part of the Antarctic Treaty System (ATS), the CCAMLR Convention is characterised by a unique sovereignty situation. The analysis thereof is complemented by a comparison with (other) regional fisheries management organisations (RFMOs) and illustrated by the difficulties in addressing illegal, unreported and unregulated (IUU) fishing. The article concludes inter alia that the CCAMLR Convention is unlike other RFMOs due to the special natural characteristics, its integration into the ATS and the ensuing sovereignty situation, and its conservationist objective. This notwithstanding, it seems justifiable to treat the CCAMLR Convention as "something more" than an RFMO for the purpose of international instruments on fisheries.


2009 ◽  
Vol 12 (6) ◽  
pp. 630-639 ◽  
Author(s):  
In Gyu Gwak ◽  
Woong sic Jung ◽  
Hak Jun Kim ◽  
Sung-Ho Kang ◽  
EonSeon Jin

Author(s):  
Oluwatoosin B. A. Agbaje ◽  
Glenn A. Brock ◽  
Zhifei Zhang ◽  
Kingsley C. Duru ◽  
Yue Liang ◽  
...  

Abstract Phosphate-shelled brachiopods differ in filter-feeding lifestyle, with Lingula anatina an active infaunal burrower, and Discinisca tenuis a shallow marine epibenthic animal. The shells of these animals are built of organophosphatic constituents, the organic fibres/sheets reinforced with calcium phosphate to provide a sophisticated ultrastructural robustness. This investigation examined the nature of the organic fibres in order to improve understanding of how living organisms produce hierarchically structured biomaterials. Unlike powdered samples commonly used in previous studies, organic fibres were isolated for the first time and the shell fractions were purified, in order to study the content and nature of the biopolymer fibres. Biochemical methods including Calcofluor staining revealed a chitin matrix. Ultrastructural analysis, thermal gravimetric analysis, and spectroscopic analyses show that the core polysaccharide framework is composed of layers of β-chitin sheets and/or fibrils that are coated with a fibrous organic matrix. There is more chitin matrix in the L. anatina shells (26.6 wt.%) compared to the D. tenuis shells (12.9 wt.%). Taken together, the data show that the chitin matrix contributes to increased skeletal strength, making L. anatina highly adapted for life as an active burrower. In comparison, D. tenuis contains less chitin and lives as attached epibenthos in a shallow marine environment. Graphical abstract First spectroscopic evidence of β-chitin sheets in recent organophosphatic brachiopods


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