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Estimate of the Basic Reproduction Number for COVID-19: A Systematic Review and Meta-analysis
Yousef Alimohamadi,Maryam Taghdir,Mojtaba Sepandi 대한예방의학회 2020 Journal of Preventive Medicine and Public Health Vol.53 No.3
Objectives: The outbreak of coronavirus disease 2019 (COVID-19) is one of the main public health challenges currently facing the world. Because of its high transmissibility, COVID-19 has already caused extensive morbidity and mortality in many countries throughout the world. An accurate estimation of the basic reproduction number (R0) of COVID-19 would be beneficial for prevention programs. In light of discrepancies in original research on this issue, this systematic review and meta-analysis aimed to estimate the pooled R0 for COVID-19 in the current outbreak. Methods: International databases (including Google Scholar, Science Direct, PubMed, and Scopus) were searched to identify studies conducted regarding the R0 of COVID-19. Articles were searched using the following keywords: “COVID-19” and “basic reproduction number” or “R0.” The heterogeneity among studies was assessed using the I2 index, the Cochran Q test, and T2. A random-effects model was used to estimate R0 in this study. Results: The mean reported R0 in the identified articles was 3.38±1.40, with a range of 1.90 to 6.49. According to the results of the random-effects model, the pooled R0 for COVID-19 was estimated as 3.32 (95% confidence interval, 2.81 to 3.82). According to the results of the meta-regression analysis, the type of model used to estimate R0 did not have a significant effect on heterogeneity among studies (p=0.81). Conclusions: Considering the estimated R0 for COVID-19, reducing the number of contacts within the population is a necessary step to control the epidemic. The estimated overall R0 was higher than the World Health Organization estimate.
Sajedi, Reza Hassan,Taghdir, Majid,Naderi-Manesh, Hossein,Khajeh, Khosro,Ranjbar, Bijan Korean Society for Biochemistry and Molecular Biol 2007 Journal of biochemistry and molecular biology Vol.40 No.3
The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.
Nikkhah, Maryam,Naderi-Manesh, Hossein,Taghdir, Majid,Talebzadeh, Mehdi,Sadeghi-Zadeh, Majid,Schaller, Janatan,Sarbolouki, Mohamad N. Korean Society for Biochemistry and Molecular Biol 2006 Journal of biochemistry and molecular biology Vol.39 No.3
In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.