Abstract:With the development of genetics, more and more research has been focused on modal organisms because of the conservative nature of biological species. Saccharomyces cerevisiae is one of the most important model organisms widely used all over the world. Recently, works published in this journal from Tsinghua University revealed a role of YMR166C in mitochondrial magnesium homeostasis in Saccharomyces cerevisiae with transposon-based genetic screen. A genome-wide screening in Saccharomyces cerevisiae for suppressor genes of MTM1 also yielded some very interesting results. Those wonderful works indicated a new era in genetic studies in China.

Abstract:Riboswitch is a novel type of posttranscriptional regulatory elements discovered by Breaker et al. in 2002. It can regulate gene expression by binding directly to small metabolites without the aid of protein molecules. Compared to normal protein-mediated regulation, riboswitch responds to metabolites more rapidly and sensitively. Its discovery opens a new world for RNA research. The recent advances in riboswitch researches were summarized, including crystal structure determination, mechanism and dynamics study, biosensor and antibacterial drug design. Topp et al. successfully reprogrammed E. coli to detect, follow, and precisely localize to a completely new chemical signal by using a synthetic riboswitch. This work provided new ideas for synthetic biology and artificial biology network. The advances in riboswitch 3D structure determination, reaction mechanism and dynamics provide useful information for rational drug design towards new generation of riboswitch-targeting antibacterials.

Abstract:The entire olfactory system, except for the olfactory sensory neurons in the nasal cavity, is an intrinsic part of the limb system, conferring olfaction many rarely known functions including the regulation of emotion, memory, and physiological and psychological states, in addition to the general function of smell. Meanwhile, the innermost anatomical structures of the sensory system and the lacking of effective tools make the study of olfactory information coding, processing, transmission and perception processes extremely difficult. The functional magnetic resonance imaging (fMRI) has been broadly used in neuroscience research, because it can repeatedly and non-invasively monitor neuronal activity in any brain region with relatively high temporal and spatial resolutions. Its application has significantly advanced our understanding of olfactory information processing at higher olfactory centers in human brain. Olfactory bulb (OB), the information coding and processing center of the olfactory system, is dedicated to and essential for olfaction. However, the relative small size of human OB, in comparison with the spatial resolution of human fMRI, has been greatly hindering our study of the mechanisms of information coding and processing in the OB. Here the application of fMRI in the olfactory system was reviewed, and focused on the small animal fMRI, its advantages and some important progresses made in the past decade.

Abstract:Calcineurin is a serine-threonine protein phosphatase that plays a pivotal role in a wide series of crucial physiologic processes such as T-cell activation, apoptosis, skeletal myocyte differentiation, and cardiac hypertrophy. A new family of regulators of calcineurin (RCANs) has been shown to modulate calcineurin activity through direct binding of it in vivo. Calcineurindependent signals are transduced to the nucleus by nuclear factor of activated T-cells (NFAT) transcription factors that undergo nuclear translocation upon dephosphorylation and promote transcriptional activation of target genes. The recent researches have revealed that RCAN1 modulating catalytic activity of calcineurin can function as an endogenous backfeed inhibitor during the calcineurin-NFAT signalling pathway. RCANs have now been implicated in several pathological conditions including Alzheimer’s disease, down syndrome and cardiac hypertrophy. In addition, the RCAN family is a rational, functional name for RCAN gene and it is proposed in 2007. It is, therefore, necessary to review the RCAN gene, RCANs and the roles of RCANs in a wide variety of diseases especially including Alzheimer’s disease. It is suggested that regulation of RCAN expression may be a new target on neurodegeneration disease.

Abstract:Aquaporins (AQP), abundant in diversity, are the member of the major intrinsic proteins (MIPs) family with extraordinary ability to transport water, and thus, play important roles in modulation of water relations in plants. The recent advances in classification, structural characteristics, and physiological functions during plant growth and development as well as the various regulation modes of the activity and the effects of several abiotic stresses (water stress and salt stress) and phytohormones (ABA, GA and ethylene) on the gene expression of AQP were reviewed.

Abstract:Magnesium homeostasis is very important to normal functions of cell and plays a role in a number of diseases such as diabetes, hypertension, chronic respiratory disorder, osteoporosis and arrhythmia. MRS2 encode a magnesium transporter protein in Saccharomyces cerevisiae and deletion of MRS2 gene results in decrease in mitochondrial magnesium concentration, groupⅡ RNA splicing defect and growth defect on nonfermentable carbon source. To obtain more information of magnesium homeostasis in mitochondria, mTn-lacZ/LEU2 transposon library was transformed into mrs2 deletion mutant to screen for suppressor genes of MRS2. YMR166C, a member of mitochondrial carrier family, was identified as a suppressor gene of MRS2. Deletion of YMR166C gene can rescue the defects of mrs2 deletion mutant such as the decrease in mitochondrial magnesium concentration, groupⅡ RNA splicing defect and growth defect on nonfermentable carbon source. For the first time it was demonstrated that YMR166C is involved in mitochondrial magnesium homeostasis.

Abstract:MTM1 gene is essential for SOD2 activity and normal mitochondrial function. MTM1 deletion results in decreased SOD2 activity, impaired mitochondrial function and growth defect on nonfermentable carbon source. A yeast genomic library was transformed into mtm1 deletion mutant to screen for suppressor genes of MTM1. The damage caused by MTM1 deletion is irreversible and even overexpression of MTM1 can not rescue the growth defect of mtm1 deletion mutant. Another screening strategy was adopted: a plasmid overexpressing MTM1 was transformed into wild type before the MTM1 gene on chromosome was deleted. The resulting strain, designated YES2MTM1, was transformed with a yeast genomic library. Transformants lost the plasmid overexpressing MTM1 after 5-FOA treatment. Yeast strains able to grow on nonfermentable carbon source with MTM1 deletion and overexpression of some DNA fragments were picked up and candidate suppressor genes were identified. Overexpression of five genes were identified to be able to rescue the growth defect on nonfermentable carbon source. The study will provide reference for MTM1 gene function and screening for suppressor of genes whose deletion result in irreversible damage.

Abstract:Parkin gene is one of the virulence gene in Parkinson’s disease. Being an E3 enzyme of ubiquitin-proteasome pathway(UPP), Parkin protein mediates many substrate proteins’ ubiquitination which has been closely linked to the pathogenesis of Parkinson’s disease. 2-oxoglutarate carrier protein(OGCP) is a mitochondrial membrane protein. Immunofluorescence and laser confocal microscope confirmed that in HEK293 cells, there are co-orientation and interaction between Parkin protein and OGCP. And Parkin protein can mediate the ubiquitination of OGCP though in vitro and in vivo ubiquitination essays. These findings suggest that OGCP may be one of the ubiquitination substrate proteins of Parkin protein and Parkin protein mediates can promote the OGCP’s ubiquitination.

Abstract:Mitochondrial respiratory oxidation is coupled with ATP synthesis. This coupling process can be broken by uncoupling protein (UCP), an integral membrane protein at mitochondrial inner membrane. Here, active rat UCP1 (rUCP1) was expressed in E. coli. Expression of rUCP1 can lower host’s growth rate. Immuno-electron microscopy proved expressed rUCP1 was mainly located on membrane. Purified rUCP1 was reconstituted into liposome and exhibited proton translocation activity. These results revealed eukaryotic UCP1 could be expressed in active form by prokaryotes and enable us to obtain enough amount of rUCP1 for structural study.

Abstract:For the computational researches on the large-scale metabolisms, MetaGen, a user-friendly utility to batch process and model the organism-specific multi-level metabolisms in KEGG into enzyme and pathway graphs, was developed. An example was given by expanding a little on the bow-tie structure of metabolic networks to show MetaGen is a useful and promising tool. MetaGen takes advantages of KEGG web service to ensure data reliability, uses relational database to accelerate the modeling process and facilitate data management, and applies advanced software modeling techniques as well as a pluggable software architecture for the easy expansion of functionalities in the future. MetaGen saves researchers from the elaboration on preparing metabolic networks for computation, which paves the way to deepen the researches on the large-scale metabolic networks. MetaGen is fully open-sourced and available at http://bnct.sourceforge.net/.

Abstract:Whether mice perceive the depth of space dependent on the visual size of object targets was explored when visual cues such as perspective and partial occlusion in space were excluded. A mouse was placed on a platform the height of which is adjustable. The platform located inside a box in which all other walls were dark exception its bottom through that light was projected as a sole visual cue. The visual object cue was composed of 4×4 grids to allow a mouse estimating the distance of the platform relative to the grids. Three sizes of grids reduced in a proportion of 2/3 and seven distances with an equal interval between the platform and the grids at the bottom were applied in the experiments. The duration of a mouse staying on the platform at each height was recorded when the different sizes of the grids were presented randomly to test whether the judgment of the mouse for the depth of the platform from the bottom was affected by the size information of the visual target. The results from all conditions of three object sizes show that time of mice staying on the platform became longer with the increase in height. In distance of 20～30 cm, the mice did not use the size information of a target to judge the depth, while mainly used the information of binocular disparity. In distance less than 20 cm or more than 30 cm, however, especially in much higher distance 50 cm, 60 cm and 70 cm, the mice were able to use the size information to do so in order to compensate the lack of binocular disparity information from both eyes. Because the mice have only 1/3 of the visual field that is binocular. This behavioral paradigm established in the current study is a useful model and can be applied to the experiments using transgenic mouse as an animal model to investigate the relationships between behaviors and gene functions.

Abstract:Estrogen receptorβ (ERβ) plays an important role in the development and progression of cardiovascular disease, but the mechanism is not clear yet. Thus, it is of great significance to discover ERβ interacting coregulators. It was identified a non-receptor tyrosine kinase c-abl as a novel ERβ cofactor. Both GST pull-down and co-IP assay indicated that ERβ interacted with c-abl in vivo and in vitro, and phosphorylation immunoblotting showed that ERβ can be phosphorylated by c-abl. Furthermore, the luciferase assay showed that c-abl enhanced ERβ mediated transcriptional activities, while c-abl inhibitor STI571 abolished c-abl mediated upregulation of ERβ transcriptional activity. These data suggest that c-abl was a novel co-activator of ERβ, which may uncover a role of ERβ signaling in cardiovascular disease.

Abstract:The influence of survivin expression on the radiosensitivity of tumor cells to high linear energy transfer (LET) radiation is investigated. Survivin-specific short-interfering RNA (siRNA) oligonucleotides were synthesized based on the survivin sequence provided by GenBank. Human hepatoma HepG2 cells were transfected with survivin-specific siRNA to inhibit its expressions. It was found that the transfection with surviving-specific siRNA increased the levels of G2/M arrest and the apoptotic rates induced by radiation in HepG2 cells. After exposure to high-LET carbon ions, a reduced clonogenic survival effect was observed in the cells treated with siRNA. These results show that survivin plays a key role in mediating the radioresistance of cells to high-LET radiation.

Abstract:The effect of colored noise on circadian oscillation and internal signal stochastic resonance(ISSR) has been studied in a Neurospora circadian clock system. The result shows that the correlation time of colored noise can affect strongly the strength of ISSR. For the case of no external signal(ES), the correlation time of colored noise plays a suppressive role for ISSR, and the suppressive role is increased with the increment of correlation time of colored noise. When the ES is injected to the system, with the increasing of the correlation time of colored noise, not only its suppressive role for ISSR is increased, but also the single peak ISSR can be transformed as internal single stochastic bi-resonance(ISSBR). There exists an optimal frequency of ES for the ISSR information amplification, while the ISSR is suppressed for another frequency of ES. In contrast to external colored noise, internal colored noise is more efficient to sustain and amplify the ISSR information. Furthermore, there exists a critical noise intensity for destroying the difference between white and colored noises.

Abstract:Proteomics has propelled the rapid development of mass spectrometry (MS) in the past ten years. Conversely, the advancement of MS has greatly expanded the horizon of proteomics research by allowing it to address questions never touched before. Standing out among the recent technological innovations in MS are electron capture dissociation (ECD) and electron transfer dissociation (ETD). These electron-based fragmentation methods have shown a great potential for analysis of proteolytic peptides as well as intact proteins. A promising future lies ahead for ECD- or ETD-based techniques in proteomics research, especially in studies of protein post-translational modifications and top-down analysis of intact proteins. The mechanism, instrumentation and application of ECD/ETD, along with the spectral characteristics and data analysis of peptides ECD/ETD spectra were reviewed. The current issues in ECD/ETD applications or method development, the challenges for software development, and the outlook of these techniques in future research were also discussed.

Abstract:Semiconductor quantum dots (QDs) as newly developed fluorescence labels are of significant importance in applications of medical and biological fields. In comparison with conventional organic fluorescence labels, QDs show super properties with adjustable fluorescence, broaden excitation and narrow emission, photochemical stability, well developed surface chemistry and bioconjugation capability, which are endowing new developing opportunities in targeting, imaging, DNA and protein detection, medicine, clinic science, biochip and biosensor in life system. This paper reviews the latest breakthrough of QDs as fluorescence labels in applications of medical and biological fields on the basis of the authors’ research works on QDs biological fluorescence imaging and toxicity, and the challenge of QDs encountered in applications of in medical and biological fields is commented as well.