Conditions optimized for the preparation of single-stranded DNA (ssDNA) employing lambda exonuclease digestion in generating DNA aptamer

The generation of DNA aptamer by Systematic Evolution of Ligands by Exponential Enrichment requires a good method of ssDNA generation. There are various methods developed to generate ssDNA such as streptavidin-biotin based separation techniques, asymmetric PCR and strand separation of the PCR product containing primer with a terminator and an extension of 20 nucleotides on denaturing urea-polyacrylamide gel. In the present investigation, we have shown the possible improvements for the regular lambda nuclease digestion under optimized conditions. Optimization of the PCR cycles, time course studies on lambda nuclease digestion and purification of the ssDNA from the lambda exonuclease digestion mixture was found to be able to recover ssDNA amounting up to 39.19 ± 2.48 % of the starting amount of dsDNA. These strategies can be applied to the techniques involving essential usage of ssDNA.     

Efficient gene disruption in Saccharomyces cerevisiae using marker cassettes with long homologous arms prepared by the restriction-free cloning strategy

Here we report an improved method for targeted gene disruption with high efficiency in S. cerevisiae, where the selection markers with long homologous arms are defined by the choice of the primer binding sites at the target locus and the disruption cassettes are constructed by restriction-free (RF) cloning strategy. Three genes, SAM1, IDH1 and IDH2, were disrupted with this method and the disruption efficiencies of SAM1 was improved several folds with much lower false-positive rates compared to the conventional one-step PCR-based gene disruption method. This approach for gene disruption cassettes construction with long flanking homologous arms may be readily applicable to facilitate targeted gene disruption in other non-conventional yeasts and fungi.     

Nucleosome structural studies

Chromatin plays a fundamental role in eukaryotic genomic regulation, and the increasing awareness of the importance of epigenetic processes in human health and disease emphasizes the need for understanding the structure and function of the nucleosome. Recent advances in chromatin structural studies, including the first structures of nucleosomes containing the Widom 601 sequence and the structure of a chromatin protein-nucleosome assembly, have provided new insight into stretching of nucleosomal DNA, nucleosome positioning, binding of metal ions, drugs and therapeutic candidates to nucleosomes, and nucleosome recognition by nuclear proteins. These discoveries ensure promising future prospects for unravelling structural attributes of chromatin.     

Chromosomal stability during ex vivo expansion of UCB CD34(+) cells

Objectives: Ex vivo expansion is a feasible strategy, which may overcome limitation of the very low frequency of haematopoietic stem/progenitor cells, in umbilical cord blood (UCB). However, both quality of cells and safety of expanded population are critical issues to be addressed for their clinical application. Hence, in this study, we evaluated genetic stability of UCB‐derived CD34⁺ cells during ex vivo culture, based on karyotype analysis, as well as its effect on cell proliferation characteristics. Materials and methods: CD34⁺ cells were isolated from human UCB samples by immunomagnetic separation and were expanded ex vivo over a 28‐day period. Expansion of total nucleate cells, CD34⁺ cells and CD34⁺ CD38^? cells was investigated. Karyotype analysis of the expanded cells from six randomly selected UCB samples was performed to evaluate their genetic stability. Results: Chromosomal abnormality of expanded cells mainly appeared by day 14, but was seldom sustained until day 28. None of the chromosomal abnormal samples displayed neoplastic proliferation, and expanded cells with altered chromosomes did not show obvious transformation phenomena according to soft agar assay. Conclusions: Ex vivo expansion could lead to occurrence of chromosomal abnormality, although here it did not produce excessive proliferative advantage of the expended cells. Importantly, chromosomal alteration seemed not to be inheritable and unlikely to result in malignant transformation. However, further in‐depth evaluation of potential clinical risks of chromosomal abnormality is warranted.     

Catalytic pyrolysis of tobacco rob: kinetic study and fuel gas produced

The pyrolysis kinetics of tobacco rob (TR) was investigated using thermogravimetric analysis (TGA) under inert atmosphere, adding chemicals (dolomite and NiO) as catalysts by catalytic-mixing method. The TGA results showed that mass loss and mass loss rates were affected by catalysts. The conversion rates increased while the activation energy decreased. Moreover, the thermal decomposition behaviors of TR were studied in the fixed-bed reactor using dolomite and NiO/γ-Al₂O₃ as catalysts by catalyst-bed method. A series of experiments had been performed to explore the effects of catalysts, and reaction temperature on the composition and yield of fuel gas. The experiments demonstrated that the catalysts had a high activity of cracking tar and hydrocarbons, as well as yielding a high fuel gas production. For both methods, dolomite and NiO revealed better catalytic performance as a view of enhancing conversion rates and increasing product gas yield.     

A comparison of membranes and enrichment strategies for microbial fuel cells

The external resistance is perhaps the easiest way to influence the operation of a microbial fuel cell (MFC). In this paper, three enrichment strategies, whereby the external resistance was fixed at: (1) a high value in order to maximize the cell voltage (U strategy); (2) a low value in order to maximize the current (I strategy); and (3) a value equal to the internal resistance of the MFC to maximize the power output (P strategy), were investigated. The I strategy resulted in increased maximum power generation and the likely reason is that electron transfer was facilitated under low external resistance, which in turn, favored the development of an electrochemically active biofilm. This experiment was conducted in a single-chamber MFC system equipped with a membrane electrode assembly, and a comparison of the performance achieved by five different membranes is also provided. Selemion was found to be a suitable alternative to Nafion.     

Microscopic structure and properties changes of cassava stillage residue pretreated by mechanical activation

This study has focused on the pretreatment of cassava stillage residue (CSR) by mechanical activation (MA) using a self-designed stirring ball mill. The changes in surface morphology, functional groups and crystalline structure of pretreated CSR were examined by using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) under reasonable conditions. The results showed that MA could significantly damage the crystal structure of CSR, resulting in the variation of surface morphology, the increase of amorphous region ratio and hydrogen bond energy, and the decrease in crystallinity and crystalline size. But no new functional groups generated during milling, and the crystal type of cellulose in CSR still belonged to cellulose I after MA.     

Leucine nutrition in animals and humans: mTOR signaling and beyond

Macronutrients, such as protein or amino acid, not only supply calories but some components may also play as signaling molecules to affect feeding behavior, energy balance, and fuel efficiency. Leucine, a branched-chain amino acid is a good example. After structural roles are satisfied, the ability of leucine to function as signal and oxidative substrate is based on a sufficient intracellular concentration. Therefore, leucine level must be sufficiently high to play the signaling and metabolic roles. Leucine is not only a substrate for protein synthesis of skeletal muscle, but also plays more roles beyond that. Leucine activates signaling factor of mammalian target of rapamycin (mTOR) to promote protein synthesis in skeletal muscle and in adipose tissue. It is also a major regulator of the mTOR sensitive response of food intake to high protein diet. Meanwhile, leucine regulates blood glucose level by promoting gluconeogenesis and aids in the retention of lean mass in a hypocaloric state. It is beneficial to animal nutrition and clinical application and extrapolation to humans.     

A comparison of the dynamics of pantothenate synthetase from M. tuberculosis and E. coli: computational studies

Pantothenate synthetase (PS) catalyzes the final step of the pantothenate pathway, in which pantothenate is formed from pantoate and β-alanine in an ATP-dependent reaction. Mycobacterium tuberculosis PS (MTB PS) is functionally a dimer and a potential target for novel antitubercular drugs. Molecular dynamics simulations show that the functional dynamics of the enzyme are dominated by motions of a flexible gate loop in the N-terminal domain and of the C-terminal domain. The gate loop motions dominate in MTB PS while the C-terminal domain motion dominates in Escherichia coli PS. Simulations also show that the correlated motions of the domains are severely compromised in the monomeric forms. Mutations that reduce the mobility of the gate loop in MTB PS and increased it in E. coli PS were designed and validated through simulations.