Simultaneous detection of multiple mutations conferring streptomycin resistance inMycobacterium tuberculosis using nanoscale engineered biomagnetites

Streptomycin-resistantMycobacterium tuberculosis has been attributed to two distinct classes of mutations, including point mutations within therpsL gene (three mutation sites) and therrs gene (seven mutation sites). We have developed an automated simultaneous detection system of multiple mutations based on thermal dissociation curve analysis for streptomycin resistance inM. tuberculosis using streptavidin-labeled bacterial magnetic particles (SA-BacMPs). With consideration for time and cost effectiveness, we used fewer PCR reactions, with a long PCR target (rpsL, 182 bp;rrs, 467 bp) including multiple mutation sites. In order to improve the amount of target DNA captured on BacMPs through streptavidin-biotin binding, several reaction conditions, such as salt species and concentration in the buffer, and reaction temperature were examined. Compared to the commonly used 1M NaCl solution, the amount of DNA captured on SA-BacMPs was about six times greater (approx 5 pmoles/50 μg BacMPs) in the 2M LiCl solution. Under these conditions, automated nucleotide discriminations of 10 targets inrpsL andrrs genes of streptomycin-resistant and wild-type strains were successfully performed at the same time.     

Identification of alcohol stress tolerance genes of <Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803 using adaptive laboratory evolution

Background

Synechocystis sp. PCC 6803 is an attractive organism for the production of alcohols, such as isobutanol and ethanol. However, because stress against the produced alcohol is a major barrier for industrial applications, it is highly desirable to engineer organisms with strong alcohol tolerance.

Results

Isobutanol-tolerant strains of Synechocystis sp. PCC 6803 were obtained by long-term passage culture experiments using medium containing 2 g/L isobutanol. These evolved strains grew on medium containing 5 g/L isobutanol on which the parental strain could not grow. Mutation analysis of the evolved strains revealed that they acquired resistance ability due to combinatorial malfunctions of slr1044 (mcpA) and slr0369 (envD), or slr0322 (hik43) and envD. The tolerant strains demonstrated stress resistance against isobutanol as well as a wide variety of alcohols such as ethanol, n-butanol, and isopentanol. As a result of introducing an ethanol-producing pathway into the evolved strain, its productivity successfully increased to 142% of the control strain.

Conclusions

Novel mutations were identified that improved the stress tolerance ability of various alcohols in Synechocystis sp. PCC 6803.

     

Regenerating islet-derived protein (Reg)3β plays a crucial role in attenuation of ileitis and colitis in mice

Regenerating islet-derived protein (Reg)3β belongs to a member of the Reg family of proteins and has pleiotropic functions, including antimicrobial activity and tissue repair. However, whether Reg3β plays a protective role in the development of colitis and ileitis has not been fully investigated. We generated transgenic mice expressing a short form of cellular FLICE-inhibitory protein (cFLIPs) that promotes necroptosis, a regulated form of cell death. cFLIPs transgenic (CFLARs Tg) mice develop severe ileitis in utero. Although Reg3β is undetectable in the small intestine of wild-type embryos, its expression is aberrantly elevated in the small intestine of CFLARs Tg embryos. To test whether elevated Reg3β attenuates or exacerbates ileitis in CFLARs Tg mice, we generated a Reg3b^?/? strain. Reg3b^?/? mice grew to adulthood without apparent abnormalities. Deletion of Reg3b in CFLARs Tg mice exacerbated the embryonic lethality of CFLARs Tg mice. Dextran sulfate sodium-induced colitis, characterized by body weight loss and infiltration of neutrophils, was exacerbated in Reg3b^?/? compared to wild-type mice. Moreover, the expression of Interleukin 6, an inflammatory cytokine and Chitinase-like 3, a marker for tissue repair macrophages was elevated in the colon of Reg3b^?/? mice compared to wild-type mice after DSS treatment. Together, these results suggest that attenuation of colitis and ileitis is a result of Reg3β′s real function.     

How do stone knappers predict and control the outcome of flaking? Implications for understanding early stone tool technology

The aim of the current study was to provide detailed data on the skill at controlling conchoidal fracture, data that may be used to help infer the processes responsible for generating the technological diversity observed in Early Stone Age sites. We conducted an experiment with modern stone knappers with different skill levels and systematically analyzed not only the products of flaking (i.e., detached flakes) but also the intentions prior to flaking, as well as the actions taken to control the shape of a flake through direct hard-hammer percussion. Only modern stone knappers with extensive knapping experience proved capable of predicting and controlling the shape of a flake, which indicated the significant difficulty of controlling the shape of flakes. Evidence was found that knowing the consequence of a strike given to a core at hand requires the acute exploration of the properties of the core and hammerstone to comply with the higher-order relationship among potential platform variables, kinetic energy of the hammerstone at impact, and flake dimension that reflects the constraints of conchoidal fracture. We argue that without this ability, controlling the shape of a flake or the organized débitage of flakes observed in some of the Early Stone Age sites may not have been possible. We further suggest that, given the difficulty and the nature of the skill, the evidence of precise control of conchoidal fracture in the Early Stone Age record may be indicative of the recurrence of a learning situation that allows the transmission of the skill, possibly through providing the opportunities for first-hand experience.     

Involvement of the Hipk family in regulation of eyeball size, lens formation and retinal morphogenesis

Members of the homeodomain-interacting protein kinase (HIPK) family are involved in various intracellular regulatory mechanisms. The present study focused on clarifying the functions of HIPK family members in ocular organization during late embryogenesis. HIPK1 and HIPK2 were expressed in the inner retina during late embryogenesis. Hipk1^+/−Hipk2^−/− mice had a greater frequency of small eyes with a lens deficiency and abnormally laminated and thickened retinas than did wild-type littermates. These data indicate that Hipk1 and Hipk2 are involved in regulation of eye size, lens formation and retinal lamination during late embryogenesis.     

Changes in expansin activity and cell wall susceptibility to expansin action during cessation of internodal elongation in floating rice

We investigated the involvement of expansin action in determining the growth rate of internodes of floating rice (Oryza sativa L.). Floating rice stem segments in which rapid internodal elongation had been induced by submergence for 2 days were exposed to air or kept in submergence for 2 more days. Both treatments reduced the elongation rate of the internodes, and the degree of reduction was much greater in air-exposed stem segments than in continually submerged segments. These rates of internodal elongation were correlated with acid-induced cell wall extensibility and cell wall susceptibility to expansins in the cell elongation zone of the internodes, but not with extractable expansin activity. These results suggest that the reduced growth rate of internodes must be due, at least in part, to the decrease in acid-induced cell wall extensibility, which can be modulated through changes in the cell wall susceptibility to expansins rather than through expansin activity. Analysis of the cell wall composition of the internodes showed that the cellulosic and noncellulosic polysaccharide contents increased in response to exposure to air, but they remained almost constant under continued submergence although the cell wall susceptibility to expansins gradually declined even under continued submergence. The content of xylose in noncellulosic neutral sugars in the cell walls of internodes was closely and negatively correlated with changes in the susceptibility of the walls to expansins. These results suggest that the deposition of xylose-rich polysaccharides into the cell walls may be related to a decrease in acid-induced cell wall extensibility in floating rice internodes through the modulation of cell wall susceptibility to expansins.     

Coordination strategies used in stone knapping

Stone tool‐use and manufacture is seen as an important skill during the evolution of our species and recently there has been increased interest in the understanding of perceptual‐motor abilities underlying this skill. This study provides further information with respect to the motor strategies used during stone knapping. Kinematics of the striking arm were recorded in expert and novice knappers while producing flakes of two different sizes. Using Uncontrolled Manifold Analysis, the results showed that knappers structure joint angle movements such that the hammer trajectory variability is minimized across trials, with experts displaying significantly smaller variability compared with novices. Principal component analysis further revealed that a single component captures the complexity of the strike and that the strike is governed by movements of the elbow and the wrist. Analysis of movement velocities indicated that both groups adjusted movement velocities according to flake size although experts used smaller hammer, wrist, and elbow velocities in both flake conditions compared with novices. The results suggest that while the gross striking movement is easy to replicate for a novice knapper, it requires prolonged training before a knapper becomes attuned to the finer details necessary for controlled flaking. © 2013 Wiley Periodicals, Inc.     

Heat denaturation increases the sensitivity of the cytomegalovirus loop‐mediated isothermal amplification method

A new protocol for CMV LAMP with an additional heat denaturation step was developed. While the sensitivity of the original CMV LAMP method was 500 copies/tube, sensitivity was increased by up to 100 copies/tube by additional heat denaturation. CMV DNA was detected in 103 of 350 samples (29.4%) by the original CMV LAMP procedure and 148 of 350 samples (42.3%) by the new CMV LAMP protocol. When the pp65 antigenemia assay was used as the standard method, the sensitivity, specificity, PPV, and NPV of the new protocol were 92.9%, 77.7%, 62.2%, and 96.5%, respectively.