Localized mRNA translation and protein association

Recent direct observations of localization of mRNAs and proteins both in prokaryotic and eukaryotic cells can be related to slowdown of diffusion of these species due to macromolecular crowding and their ability to aggregate and form immobile or slowly mobile complexes. Here, a generic kinetic model describing both these factors is presented and comprehensively analyzed. Although the model is non-linear, an accurate self-consistent analytical solution of the corresponding reaction-diffusion equation has been constructed, the types of localized protein distributions have been explicitly shown, and the predicted kinetic regimes of gene expression have been classified.     

ncRNA-mediated bistability in the synthesis of hundreds of distinct mRNAs and proteins

The kinetics of gene expression can be bistable due to the feedback between the mRNA and protein formation. In eukaryotic cells, the interplay between mRNAs and proteins can be influenced by non-coding RNAs. Some of these RNAs, e.g., microRNAs, may target hundreds of distinct mRNAs. The model presented here shows how a non-coding RNA can be used as a mediator in order to involve numerous mRNAs and proteins into a bistable network.     

GAP-43 mRNA detection by in situ hybridization, direct and indirect in situ RT-PCR in hippocampal and cerebellar tissue sections of adult rat brain

The growth-associated protein GAP-43 is a presynaptic membrane phosphoprotein that is expressed at high levels during development and axonal growth. To evaluate the cellular distribution of GAP-43 mRNA in the hippocampus and cerebellum of adult rats we applied in situ hybridization (ISH) as well as direct and indirect in situ RT-PCR using biotin as a reporter molecule. ISH resulted in a positive signal in most cerebellar granular cells and in 30% of hippocampal CA3 neurons. Direct in situ RT-PCR yielded cells with strong signals in every region investigated, with elevated background levels most likely related to incorporation of labeled nucleotides into non-specific amplicons through internal priming and DNA repair activity. Indirect in situ RT-PCR turned out to be the best approach for detecting GAP-43 mRNA positive cells. Cerebellar cells exhibiting a positive signal for GAP-43 mRNA were of the granular cell type (98%). Hippocampal neurons with a positive reaction for GAP-43 mRNA included all the neuron groups analyzed, namely CA1 (99%) and CA3 pyramidal cells (94%) and dentate gyrus granule cells (92%). Dentate gyrus granule cells have not tested positive for GAP-43 mRNA detection by molecular morphology analysis. These data show that in normal rats GAP-43 mRNA is present in different cell populations of hippocampal formation, supporting the role of this protein in the ongoing processes of synaptic plasticity.     

Layer-by-Layer-Assembled Capsule Size Affects the Efficiency of Packaging and Delivery of Different Genetic Cargo

The lack of an efficient and versatile intracellular nucleic acids delivery platform impedes the clinical implementation of gene therapy. Advances in layer-by-layer (LbL) technology have led to the production of LbL polymer capsules, a promising universal delivery tool. The biocompatibility, sufficient packaging capacity, safety, low cost, and high variability of structure and composition of the LbL capsules make it possible to meet the requirements for clinical-grade nonviral gene transfer. Here, the possibility of polymeric LbL capsules of different sizes (micrometer and sub-micrometer-sized) to serve as universal nonviral carriers for messenger RNA (mRNA) and small interfering RNA (siRNA) is considered. In particular, the internalization of capsules into human mesenchymal stem cells (hMSCs, as an example of adult primary stem cells), capsule uptake, and intracellular delivery of mRNA and siRNA is studied. Importantly, the use of micrometer- or sub-micrometer-sized polymer capsules (MicCaps and SubCaps) allows the mRNA or siRNA to be packaged and transferred into hMSCs with high efficiency. While the uptake efficiency is comparable between MicCaps and SubCaps, the latter are significantly more efficient than MicCap when transferring siRNAs. These results demonstrate the potential of the LbL capsules as a universal gene delivery platform, which can be tuned according to the properties of genetic cargo.     

How the Number of Alleles Influences Gene Expression

The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.     

Enhanced effect of microdystrophin gene transfection by HSV-VP22 mediated intercellular protein transport

Background

Duchenne musclar dystrophy (DMD) is an X-linked recessive disease caused by mutations of dystrophin gene, there is no effective treatment for this disorder at present. Plasmid-mediated gene therapy is a promising therapeutical approach for the treatment of DMD. One of the major issues with plasmid-mediated gene therapy for DMD is poor transfection efficiency and distribution. The herpes simplex virus protein VP22 has the capacity to spread from a primary transduced cell to surrounding cells and improve the outcome of gene transfer. To improve the efficiency of plasmid-mediated gene therapy and investigate the utility of the intercellular trafficking properties of VP22-linked protein for the treatment for DMD, expression vectors for C-terminal versions of VP22-microdystrophin fusion protein was constructed and the VP22-mediated shuttle effect was evaluated both in vitro and in vivo.

Results

Our results clearly demonstrate that the VP22-microdystrophin fusion protein could transport into C2C12 cells from 3T3 cells, moreover, the VP22-microdystrophin fusion protein enhanced greatly the amount of microdystrophin that accumulated following microdystrophin gene transfer in both transfected 3T3 cells and in the muscles of dystrophin-deficient (mdx) mice.

Conclusion

These results highlight the efficiency of the VP22-mediated intercellular protein delivery for potential therapy of DMD and suggested that protein transduction may be a potential and versatile tool to enhance the effects of gene delivery for somatic gene therapy of DMD.     

Oscillatory kinetics of gene expression: Protein conversion and slow mRNA transport

The negative feedback between mRNA and regulatory-protein production may result in oscillations in the kinetics of gene expression if the mRNA-protein interplay includes protein conversion. Using a mean-field kinetic model, we show that such oscillations can be amplified due to limitations of the mRNA transport between the nucleus and cytoplasm. This effect may be dramatic for the mRNA population in the nucleus. The article is published in the original.     

Measuring protein self-diffusion in protein-protein mixtures using a pulsed gradient spin-echo technique with WATERGATE and isotope filtering

Here we report a modified pulsed gradient spin-echo (PGSTE) pulse sequence to measure diffusion coefficients. This approach incorporates WATERGATE combined with isotopic filtering into a standard PGSTE experiment. Doing this eliminates much of the disadvantages from the combination of diffusion encoding and heteronuclear selection intervals and allows for facile modification of the diffusion pulse sequence with flexibility of the time period between RF pulses. The new diffusion pulse sequence is demonstrated using an 15N-labeled peptide and an 15N-labeled protein in a mixture with a protein of similar size.     

固定化细胞的制备以及性能实验研究

本文对固定化光合细胞的制备工艺以及包埋细菌时固定化颗粒的结构、扩散性能作了初步的研究,采用PVA和海藻酸纳为包埋剂为可视化实验制作了一种完全透明的固定化颗粒,采用吸渗法测其孔隙率,并测定了颗粒中葡萄糖的扩散系数.     

Early raise of BDNF in hippocampus suggests induction of posttranscriptional mechanisms by antidepressants

Background  

The neurotrophin BDNF has been implicated in the regulation of neuroplasticity, gene expression, and synaptic function in the adult brain, as well as in the pathophysiology of neuropsychiatric disorders and the mechanism of action of antidepressants. Antidepressant treatments have been shown to increase the expression of BDNF mRNA, although the changes measured were found to be different depending on various factors. A few studies only have measured levels of BDNF protein after antidepressant treatments, and poor correlation was found between mRNA and protein changes. We studied the time course of expression of BDNF mRNA and protein during drug treatments, in order to elucidate the temporal profile of regulation of this effector and whether mRNA and protein levels correlate. Rat groups were treated for 1, 2 or 3 weeks with fluoxetine or reboxetine; in additional groups drug treatment was followed by a washout week (3+1). Total BDNF mRNA was measured by Real Time PCR, pro- and mature BDNF proteins were measured by Western blot.     

晶硅太阳电池中Fe-B对与少子寿命、陷阱浓度及内量子效率的相关性

以太阳电池级直拉单晶硅片为材料,利用瞬态微波反射光电导衰减仪研究了硅片分别经过单、双面扩散后Fe-B对与少子寿命τ、陷阱浓度及制备成电池的内量子效率（IQE）的相关性.对于单面扩散后的样品,Fe-B对浓度分布在较大程度上决定了少子寿命分布;对于双面扩散后的样品,Fe-B对浓度显著降低（在135×10¹¹ cm^-3左右）,已不及其他杂质和缺陷对少子寿命的影响.结合瞬态微波衰减信号和陷阱模型,对单、双面吸杂前后硅片的陷阱浓度进行数值计算,发现经过扩散 关键词： 少子寿命 陷阱浓度 内量子效率 Fe-B对