Cysteine 295 indirectly affects Ni coordination of carbon monoxide dehydrogenase-II C-cluster

A unique [Ni–Fe–S] cluster (C-cluster) constitutes the active center of Ni-containing carbon monoxide dehydrogenases (CODHs). His²⁶¹, which coordinates one of the Fe atoms with Cys²⁹⁵, is suggested to be the only residue required for Ni coordination in the C-cluster. To evaluate the role of Cys²⁹⁵, we constructed CODH-II variants. Ala substitution for the Cys²⁹⁵ substitution resulted in the decrease of Ni content and didn’t result in major change of Fe content. In addition, the substitution had no effect on the ability to assemble a full complement of [Fe–S] clusters. This strongly suggests Cys²⁹⁵ indirectly and His²⁶¹ together affect Ni-coordination in the C-cluster.     

A Phytotoxin,Betaenone C,and Its Related Metabolites of Phoma betae Fr

For rough quantitative analysis of genetically modified maize contents, rapid methods for measurement of the copy numbers of the cauliflower mosaic virus 35S promoter region (P35S) and MON810 construct-specific gene (MON810) using a combination of a capillary-type real-time PCR system with a plasmid DNA were established. To reduce the characteristic differences between the plasmid DNA and genomic DNA, we showed that pretreatment of the extracted genomic DNA by a combination of sonication and restriction endonuclease digestion before measurement is effective. The accuracy and reproducibility of this method for MON810 content (%) at a level of 5.0% MON810 mixed samples were within a range from 4.26 to 5.11% in the P35S copy number quantification. These methods should prove to be a useful tool to roughly quantify GM maize content.     

A Comparison of the Unfolded Protein Response in Solid-State with Submerged Cultures of Aspergillus oryzae

The unfolded protein response (UPR) is a regulatory system to maintain the homeostasis of ER functions. Here we report a comparison of express levels of UPR relevant genes in Aspergillus oryzae between solid-state and submerged cultivation. The results were that up-regulation of the UPR mechanism in solid-state culture was higher than in submerged culture (heat-shock or non-stress conditions). This might have been a result of changing culture conditions.     

A Simple and Efficient Method for High Fidelity PCR Cloning Using Antibody-neutralizing Technology

We introduce the TA cloning antibody method for the high-fidelity PCR product amplified by family B DNA polymerase without purification. This method uses antibodies and Thermus aquaticus (Taq) DNA polymerase. The antibodies can inhibit only the activity of family B DNA polymerase, and Taq can co-work for A-tailing. This method has nearly cloning efficiency to that of the PCR product of Taq.     

Degradation of Barley Glucan and Lichenan by a Bacillus pumilus Enzyme

A bacterial strain was isolated from soil, which rapidly degraded purified barley β-glucan as well as lichenan. The strain belonged to Bacillus pumilus, and some authentic strains of this species were also shown to hydrolyze the gluean. An enzyme active on the above substrates but not on laminaran and on CM-cellulose was partially purified from the culture fluid. This enzyme, about 27,000 in molecular weight, was found to cleave a β-(1 → 4) linkage adjacent to a β-(1 → 3) in the polymers. It was suggested that only an enzyme of this type should be called a ‘lichenanase’ and discriminated from cellulases and laminaranases.     

Formaldehyde induces toxic effects and regulates the expression of damage response genes in BM-MSCs

In this study, we assessed the toxic effects of formaldehyde （FA） on mouse bone marrow mesenchymai stem cells （BM- MSCs）. Cytotoxicity was measured by using MTT assay. DNA strand breakage was detected by standard alkaline comet assay and comet assay modified with proteinase K （PK）. DNA-protein crosslinks （DPCs） were detected by KCI-SDS precipitation assay. We found that FA at a con- centration from 75 to 200 μM inhibited cell survival and induced DPCs over 125 μM. The PK-modified comet assay showed that FA-induced DNA strand breakage was increased in a dose-dependent manner from 75 to 200 μM. On the other hand, standard alkaline comet assay showed that DNA strand breakage was decreased with FA concen- tration over 125 μM. We confirmed by using Pearson cor- relation that there was a negative linear correlation between DPCs and survival rate （r = -0.987, P 〈 0.01） and positive linear relationships between DPCs and （i） sister chromatid exchange and （ii） micronucleus （r = 0.995, P〈 0.01; r = 0.968, P〈 0.01）. DNA damage RTz profiler polymerase chain reaction array was used to investigate the changes in the expression of damage response genes. Xpa and Xpc of the nucleotide excision repair pathway and Brca2, Rad51, and Xrcc2 of the homologous recombination pathway were all up-regulated in both 75 and 125 μM FA. However, the same genes were down-regulated with 175 μM FA. The expressions of Chekl and Husl, which are involved in cell cycle regulation, were altered in the same manner with 75, 125, and 175 μM FA. These results indicated that Xpa, Xpc, Brca2, Rad51, Xrcc2, Chekl, and Husl were essential for the BM-MSCs to counteract the effects of FA.     

Combining ethidium monoazide treatment with real-time PCR selectively quantifies viable Batrachochytrium dendrobatidis cells

Detection of the lethal amphibian fungus Batrachochytrium dendrobatidis relies on PCR-based techniques. Although highly accurate and sensitive, these methods fail to distinguish between viable and dead cells. In this study a novel approach combining the DNA intercalating dye ethidium monoazide (EMA) and real-time PCR is presented that allows quantification of viable B. dendrobatidis cells without the need for culturing. The developed method is able to suppress real-time PCR signals of heat-killed B. dendrobatidis zoospores by 99.9 % and is able to discriminate viable from heat-killed B. dendrobatidis zoospores in mixed samples. Furthermore, the novel approach was applied to assess the antifungal activity of the veterinary antiseptic F10^® Antiseptic Solution. This disinfectant killed B. dendrobatidis zoospores effectively within 1 min at concentrations as low as 1:6400.     

Comparison of droplet digital PCR to real-time PCR for quantification of hepatitis B virus DNA

Quantitative real-time PCR (qPCR) has been widely implemented for clinical hepatitis B viral load testing, but a lack of standardization and relatively poor precision hinder its usefulness. Droplet digital PCR (ddPCR) is a promising tool that offers high precision and direct quantification. In this study, we compared the ddPCR QX100 platform by Bio-Rad with the CFX384 Touch Real-Time PCR Detection System (Bio-Rad, USA) to detect serial plasmid DNA dilutions of known concentrations as well as HBV DNA extracted from patient serum samples. Both methods showed a high degree of linearity and quantitative correlation. However, ddPCR assays generated more reproducible results and detected lower copy numbers than qPCR assays. Patient sample quantifications by ddPCR and qPCR were highly agreeable based on the Bland–Altman analysis. Collectively, our findings demonstrate that ddPCR offers improved analytical sensitivity and specificity for HBV measurements and is suitable for clinical HBV detection.     

Real‐time PCR identification of the ambrosia beetles,Trypodendron domesticum (L.) and Trypodendron lineatum (Olivier) (Coleoptera: Scolytidae)

The European hardwood ambrosia beetle (Trypodendron domesticum) and the striped ambrosia beetle (Trypodendron lineatum) are wood‐boring pests that can cause serious damage to lumber, resulting in a need for management of these pests in logging and lumber industries. Natural populations of ambrosia beetles exist throughout the world, but movement of ambrosia beetles into new habitats, particularly via international trade, can result in the establishment of invasive species that have the potential to spread into new territory. Efforts to monitor ambrosia beetle populations are time‐consuming and could be greatly enhanced by the use of molecular methods, which would provide accurate and rapid identification of potentially problematic species. Here, we present new real‐time PCR assays for the detection and identification of T. domesticum and T. lineatum. The methods described herein can be used with a variety of sampling strategies to enable timely and well‐informed decision‐making in efforts to control these ambrosia beetles.