Interaction of IFNλR1 with TRAF6 regulates NF-κB activation and IFNλR1 stability

IFNλR1 is a member of the class II cytokine receptor family, and it associates with IL‐10R2 to form a functional receptor complex, IFNλR. This receptor complex transduces signals from IFNλs (IFNλ1, IFNλ2, and IFNλ3), promoting antiviral and antiproliferative activities similar to those of type I IFNs. In an effort to further understand signal transduction through IFNλR1, we used bioinformatics analysis and identified a tumor necrosis factor receptor‐associated factor 6 (TRAF6)‐binding motif in the intracellular domain of IFNλR1. In subsequent immunoprecipitation and GST pull‐down assays, IFNλR1 was shown to immunoprecipitate with TRAF6 and was pulled down by GST‐TRAF6. Endogenous IFNλR1 and TRAF‐6 interaction implies that these proteins really interact in the cells. This interaction was abrogated upon mutation of the TRAF6‐binding motif in IFNλR1. Furthermore, the interaction between IFNλR1 and TRAF6 inhibited TRAF6‐induced NF‐κB activation, likely due to a reduction in TRAF6 autoubiquitination. Moreover, co‐expression of IFNλR1 with TRAF6 significantly increased the stability of IFNλR1, thereby prolonging its half‐life and enhancing its steady‐state level in cultured cells. J. Cell. Biochem. 113: 3371–3379, 2012. © 2012 Wiley Periodicals, Inc.     

Web Apollo: a web-based genomic annotation editing platform

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.     

Hydraulic loading,stability and water quality of Nakivubo wetland,Uganda

Nakivubo wetland, which has performed tertiary water treatment for Kampala city for the past 40 years, is ecologically stressed by agricultural and infrastructural developments. Field studies were carried out to assess the hydraulic loading, pollution profile, stability and water quality of this wetland. The upper and lower Nakivubo wetland receive 4.13?7.66 × 10⁴ and 3.50?10.32 × 10⁴m³/day of water respectively, of which 48.3–57.9% of total hydraulic loading to the upper wetland was carried by sampling station S1. The influent water to the upper wetland had a total BOD₅ and NH₄-N loading ranging from 2.6?4.4 × 10³kg BOD/day and 0.79?1.68 × 10³kg NH₄-N/day respectively. The National Water and Sewerage Corporation's effluent constituted a large proportion of BOD and NH₄-N loading into Nakivubo wetland. Zinc, copper and chromium were detected in trace amounts at most sampling stations. However, lead was occasionally detected at Kibira channel (station S5) at a concentration of 0.4mg/l, which is higher than the permitted Ugandan discharge limit of 0.1mg/l (NEMA 1999). The wetland showed a very high removal efficiency for BOD, ranging from 77.4%–86.3%, compared to ammonium-N which ranged from ?66.1% to 33.1% indicating limitations with the nitrification process. A low self-purification for zinc, copper and chromium was also observed in the upper Nakivubo wetland, possibly due to poor plant-wastewater interaction resulting from wetland drainage. In the lower Nakivubo wetland conductivity and dissolved oxygen were generally higher in papyrus- than in Miscanthidium-vegetated zones. However, the BOD and ammonium-N loadings did not vary significantly (P = 0.217 and P = 0.359 respectively) between the two vegetated zones.     

Hyperglycemia accelerates ATP‐binding cassette transporter A1 degradation via an ERK‐dependent pathway in macrophages

An elevation in blood glucose concentration leads to increased risk of developing diabetes‐associated atherosclerotic cardiovascular disease due to an excessive accumulation of cholesterol in arterial macrophages. ATP‐binding cassette transporter A1 (ABCA1) is an atheroprotective protein that mediates the export of cholesterol from macrophages. The present study aims to investigate the effect of hyperglycemia on the regulation of ABCA1 expression and to explore its underlying mechanisms of regulation in macrophages. Our results show that high glucose activates the extracellular signal‐regulated kinases (ERK) signaling pathway via reactive oxygen species (ROS) production, which in turn down‐regulates ABCA1 mRNA and protein expression. This down‐regulation is mediated by accelerating ABCA1 mRNA and protein degradation in macrophages exposed to high concentrations of glucose. Our results provide evidence for the first time that hyperglycemia inhibits ABCA1 expression by ERK‐modulated ABCA1 mRNA and protein stability. Overall, these results provide a mechanism for hyperglycemia‐induced reduction in ABCA1 expression, which suggests a promising strategy for the treatment of diabetes‐associated atherosclerosis. J. Cell. Biochem. 114: 1364–1373, 2013. © 2012 Wiley Periodicals, Inc.     

CRISPR Editing in Biological and Biomedical Investigation

The CRISPR (clustered regularly interspaced short palindromic repeat)‐Cas (CRISPR‐associated protein) system, a prokaryotic RNA‐based adaptive immune system against viral infection, is emerging as a powerful genome editing tool in broad research areas. To further improve and expand its functionality, various CRISPR delivery strategies have been tested and optimized, and key CRISPR system components such as Cas protein have been engineered with different purposes. Benefiting from more in‐depth understanding and further development of CRISPR, versatile CRISPR‐based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine. In biological research area, CRISPR has been widely adopted in both fundamental and applied research fields, such as genomic and epigenomic modification, genome‐wide screening, cell and animal research, agriculture transforming, livestock breeding, food manufacture, industrial biotechnology, and gene drives in disease agents control. In biomedical research area, CRISPR has also shown its extensive applicability in the establishment of animal models for genetic disorders, generation of tissue donors, implementation of antimicrobial and antiviral studies, identification and assessment of new drugs, and even treatment for clinical diseases. However, there are still several problems to consider, and the biggest concerns are the off‐target effects and ethical issues of this technology. In this prospect article, after highlighting recent development of CRISPR systems, we outline different applications and current limitations of CRISPR in biological and biomedical investigation. Finally, we provide a perspective on future development and potential risks of this multifunctional technology. J. Cell. Biochem. 119: 52–61, 2018. © 2017 Wiley Periodicals, Inc.     

Comparative genomic structures of Mycobacterium CRISPR-Cas

Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of many archaea and bacteria, conferring acquired immunity against invading nucleic acids. CRISPR might be indicative of the bacterial niche adaptation and evolutionary. Mycobacterium is an important genus occupying diverse niches with profound medical and environmental significance. To present a comparative genomic landscape of the Mycobacterium CRISPR, the feature of mycobacterium CRISPR structures with sequenced complete genomes were bioinformatically analyzed. The results show that CRISPR structures can be found among 14 mycobacteria, and all loci are chromosomally located. Long CRISPRs present in three species, namely M. tuberculosis, M. bovis, and M. avium. Integrated CRISPR-Cas system can only be found in M. tuberculosis and M. bovis, with highly conserved repeat sequences, very short leaders, and promoterless. M. tuberculosis and M. bovis repeat sequences cannot form stable RNA secondary structure, consistent with a Cas6-binding sequence. M. avium repeat sequences can form classical stem-loop structure. A three-step model of M. tuberculosis CRISPR-Cas system action was put forward based on the composition and function of cas genes cluster. M. tuberculosis and M. bovis CRISPRs might interfere with the invading nucleic acids, but have somehow lost the capacity to incorporate new spacers and co-evolve with corresponding mycobacteriophages.