Functions of family-22 carbohydrate-binding module in Clostridium thermocellum Xyn10C

Clostridium thermocellum xylanase Xyn10C (formerly XynC) is a modular enzyme, comprising a family-22 carbohydrate-binding module (CBM), a family-10 catalytic module of the glycoside hydrolases, and a dockerin module responsible for cellulosome assembly consecutively from the N-terminus. To study the functions of the CBM, truncated derivatives of Xyn10C were constructed: a recombinant catalytic module polypeptide (rCM), a family-22 CBM polypeptide (rCBM), and a polypeptide composed of the family-22 CBM and CM (rCBM-CM). The recombinant proteins were characterized by enzyme and binding assays. Although the catalytic activity of rCBM-CM toward insoluble xylan was four times higher than that of rCM toward the same substrate, removal of the CBM did not severely affect catalytic activity toward soluble xylan or beta-1,3-1,4-glucan. rCBM showed an affinity for amorphous celluloses and insoluble and soluble xylan in qualitative binding assays. The optimum temperature of rCBM-CM was 80 degrees C and that of rCM was 60 degrees C. These results indicate that the family-22 CBM of C. thermocellum Xyn10C not only was responsible for the binding of the enzyme to the substrates, but also contributes to the stability of the CM in the presence of the substrate at high temperatures.     

Corrigendum to “Synthesis,structure-activity relationship and molecular docking studies of 3-O-flavonol glycosides as cholinesterase inhibitors” [Bioorg. Med. Chem. 26 (12) (2018) 3696–3706]

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Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins

Proteins are often monitored by combining a fluorescent polypeptide tag with the target protein. However, due to the high molecular weight and immunogenicity of such tags, they are not suitable choices for combining with fusion proteins such as immunotoxins. In this study, we designed a polypeptide sequence with a dual role (it acts as both a linker and a fluorescent probe) to use with fusion proteins. Two common fluorescent tag sequences based on tetracysteine were compared to a commonly used rigid linker as well as our proposed dual-purpose sequence. Computational investigations showed that the dual-purpose sequence was structurally stable and may be a good choice to use as both a linker and a fluorescence marker between two moieties in a fusion protein.     

DMRFusion: A differentially methylated region detection tool based on the ranked fusion method

DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylation analysis of DMRs on methylation sequencing data. This tool is designed base on the integration of several ranking methods; Information gain, Between versus within Class scatter ratio, Fisher ratio, Z-score and Welch's t-test. In this study, DMRFusion on reduced representation bisulfite sequencing (RRBS) data in chronic lymphocytic leukemia cancer displayed 30 nominated regions and CpG sites with a maximum methylation difference detected in the hypermethylation DMRs. We realized that DMRFusion is able to process methylation sequencing data in an efficient and accurate manner and to provide annotation and visualization for DMRs with high fold difference score (p-value and FDR < 0.05 and type I error: 0.04).     

Gender specificity of a genetic variant of angiotensin-converting enzyme and risk of coronary artery disease

Etiological factors for coronary artery disease (CAD) involve a wide range of gene and environmental interactions. One of the systems being implicated in the pathophysiology of CAD is the renin-angiotensin system (RAS). However, the genetic polymorphisms of this system have not been widely studied in Iranian patients diagnosed with CAD. The aim of this study was to assess the relationship between six gene polymorphisms of RAS components and CAD in a sample of Iranian population. A total of 374 participants were enrolled in a case/control study. The presence of CAD was determined by coronary angiography. Genotyping of six RAS gene polymorphisms was performed using a modified PCR–RFLP method. Our results revealed, for the first time, a significant independent association of angiotensin-converting enzyme (ACE) A-240T polymorphism and incidence of CAD among Iranian women (P = 0.005, OR = 20.4, 95 % CI = 2.49–41.2). There has also been a significant difference in genotype distribution of ACE A-240T (P = 0.008) and angiotensin II receptor type 2 C3123A polymorphism (P = 0.032) in Iranian female participants. In conclusion, TT genotype of ACE A-240T seems to be a genetic risk factor for CAD in Iranian women.     

Enhanced reconstruction of rat calvarial defects achieved by plasma-treated electrospun scaffolds and induced pluripotent stem cells

Tissue engineering with a combination of stem cells and nanofibrous scaffolds has attracted interest with regard to bone regeneration applications. In the present study, human induced pluripotent stem cells (iPSCs) were cultured on polymeric nanofibrous polyethersulfone (PES) with and without plasma treatment. The capacity of PES and plasma-treated PES (Plasma-PES) scaffolds to support the proliferation and osteogenic differentiation of iPSCs was investigated by MTT assay and for common osteogenic markers such as alkaline phosphatase activity, calcium mineral deposition and bone-related genes. Plasma-PES scaffolds with or without iPSCs were subsequently used to evaluate bone regeneration of critical-size defects in the rat by digital mammography, multislice spiral-computed tomography imaging and histological analysis. The results of in vitro analysis showed that plasma treatment significantly enhanced iPSC proliferation and osteogenesis. After 8 weeks of iPSC-loaded Plasma-PES implantation, no mortality or complication was observed in animals or at the site of surgery. Imaging analysis revealed more extensive bone reconstruction in rats receiving nanofibers compared with untreated control groups. Moreover, Plasma-PES seeded with iPSCs induced the highest regeneration of bone defects among all groups. These findings were confirmed by histological staining. Affective osseointegration was observed in implanted scaffolds. Thus, plasma-treated nanofibrous scaffolds are suitable tissue-engineered matrices for supporting the proliferation and osteogenic differentiation of iPSCs and might also be appropriate for the reconstruction of bone defects.     

A test of time–place learning in single and grouped great sturgeon Huso huso

Although there exists a large body of knowledge on the ecology, physiology, and nutrition of great sturgeon, time–place learning has thus far not been examined in this species and other sturgeons. The aim of the present study is to evaluate whether individual or grouped juvenile great sturgeons are able to associate time and place of food delivery when examined under light and dark conditions. During a 30-day period, food was made available to the sturgeons twice a day or twice a night, in the first time in one side of the tank and in the second time in the opposite side of the tank. Food was withheld on test days to assess time–place learning by the fish. The results of the present study indicate that, at both the group and individual levels, great sturgeons are not able to clearly demonstrate time–place learning under the conditions examined.