TNFAIP1 contributes to the neurotoxicity induced by Aβ25–35 in Neuro2a cells

Background: Amyloid-beta (Aβ) accumulation is a hallmark of Alzheimer’s disease (AD) that can lead to neuronal dysfunction and apoptosis. Tumor necrosis factor, alpha-induced protein 1 (TNFAIP1) is an apoptotic protein that was robustly induced in the transgenic C. elegans AD brains. However, the roles of TNFAIP1 in AD have not been investigated. Results: We found TNFAIP1 protein and mRNA levels were dramatically elevated in primary mouse cortical neurons and Neuro2a (N2a) cells exposed to Aβ25–35. Knockdown and overexpression of TNFAIP1 significantly attenuated and exacerbated Aβ25–35-induced neurotoxicity in N2a cells, respectively. Further studies showed that TNFAIP1 knockdown significantly blocked Aβ25–35-induced cleaved caspase 3, whereas TNFAIP1 overexpression enhanced Aβ25–35-induced cleaved caspase 3, suggesting that TNFAIP1 plays an important role in Aβ25–35-induced neuronal apoptosis. Moreover, we observed that TNFAIP1 was capable of inhibiting the levels of phosphorylated Akt and CREB, and also anti-apoptotic protein Bcl-2. TNFAIP1 overexpression enhanced the inhibitory effect of Aβ25–35 on the levels of p-CREB and Bcl-2, while TNFAIP1 knockdown reversed Aβ25–35-induced attenuation in the levels of p-CREB and Bcl-2. Conclusion: These results suggested that TNFAIP1 contributes to Aβ25–35-induced neurotoxicity by attenuating Akt/CREB signaling pathway, and Bcl-2 expression

Identification of target genes of transcription factor activator protein 2 gamma in breast cancer cells

<p>Abstract</p> <p>Background</p> <p>Activator protein 2 gamma (AP-2γ) is a member of the transcription factor activator protein-2 (AP-2) family, which is developmentally regulated and plays a role in human neoplasia. AP-2γ has been found to be overexpressed in most breast cancers, and have a dual role to inhibit tumor initiation and promote tumor progression afterwards during mammary tumorigensis.</p> <p>Methods</p> <p>To identify the gene targets that mediate its effects, we performed chromatin immunoprecipitation (ChIP) to isolate AP-2γ binding sites on genomic DNA from human breast cancer cell line MDA-MB-453.</p> <p>Results</p> <p>20 novel DNA fragments proximal to potential AP-2γ targets were obtained. They are categorized into functional groups of carcinogenesis, metabolism and others. A combination of sequence analysis, reporter gene assays, quantitative real-time PCR, electrophoretic gel mobility shift assays and immunoblot analysis further confirmed the four AP-2γ target genes in carcinogenesis group: ErbB2, CDH2, HPSE and IGSF11. Our results were consistent with the previous reports that ErbB2 was the target gene of AP-2γ. Decreased expression and overexpression of AP-2γ in human breast cancer cells significantly altered the expression of these four genes, indicating that AP-2γ directly regulates them.</p> <p>Conclusion</p> <p>This suggested that AP-2γ can coordinate the expression of a network of genes, involving in carcinogenesis, especially in breast cancer. They could serve as therapeutic targets against breast cancers in the future.</p

Current gene therapy using viral vectors for chronic pain

The complexity of chronic pain and the challenges of pharmacotherapy highlight the importance of development of new approaches to pain management. Gene therapy approaches may be complementary to pharmacotherapy for several advantages. Gene therapy strategies may target specific chronic pain mechanisms in a tissue-specific manner. The present collection of articles features distinct gene therapy approaches targeting specific mechanisms identified as important in the specific pain conditions. Dr. Fairbanks group describes commonly used gene therapeutics (herpes simplex viral vector (HSV) and adeno-associated viral vector (AAV)), and addresses biodistribution and potential neurotoxicity in pre-clinical models of vector delivery. Dr. Tao group addresses that downregulation of a voltage-gated potassium channel (Kv1.2) contributes to the maintenance of neuropathic pain. Alleviation of chronic pain through restoring Kv1.2 expression in sensory neurons is presented in this review. Drs Goins and Kinchington group describes a strategy to use the replication defective HSV vector to deliver two different gene products (enkephalin and TNF soluble receptor) for the treatment of post-herpetic neuralgia. Dr. Hao group addresses the observation that the pro-inflammatory cytokines are an important shared mechanism underlying both neuropathic pain and the development of opioid analgesic tolerance and withdrawal. The use of gene therapy strategies to enhance expression of the anti-pro-inflammatory cytokines is summarized. Development of multiple gene therapy strategies may have the benefit of targeting specific pathologies associated with distinct chronic pain conditions (by Guest Editors, Drs. C. Fairbanks and S. Hao)

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Abstract Background Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs’ function and conservation is really intriguing. Results We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. Conclusions By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human

GCEN: An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation

Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expression network and to predict gene function, we developed GCEN, a cross-platform command-line toolkit developed with C++. It is an efficient and easy-to-use solution that will allow everyone to perform gene co-expression network analysis without the requirement of sophisticated programming skills, especially in cases of RNA-Seq research and lncRNAs function annotation. Because of its modular design, GCEN can be easily integrated into other pipelines

Mechanism and Origins of <i>Z</i> Selectivity of the Catalytic Hydroalkoxylation of Alkynes via Rhodium Vinylidene Complexes To Produce Enol Ethers

We report the first theoretical study of transition-metal-catalyzed hydroalkoxylation of alkynes to produce enol ethers. The study utilizes density functional theory calculations (M06) to elucidate the mechanism and origins of <i>Z</i> selectivity of the anti-Markovnikov hydroalkoxylation of terminal alkynes with a Rh­(I) 8-quinolinolato carbonyl chelate (<b>1cat</b>). The chosen system is, without any truncation, the realistic reaction of phenylacetylene and methanol with <b>1cat</b>. Initiation of <b>1cat</b> through phenylacetylene substitution for carbonyl generates the active catalyst, a Rh­(I) η²-alkyne complex (<b>3</b>), which tautomerizes via an indirect 1,2-hydrogen shift to the Rh­(I) vinylidene complex <b>4</b>. The oxygen nucleophile methanol attacks the electrophilic vinylidene C_α, forming two stereoisomeric Rh­(I) vinyl complexes (<b>15</b> and <b>16</b>), which ultimately lead to the (<i>Z</i>)- and (<i>E</i>)-enol ether products. These complexes undergo two ligand-mediated proton transfers to yield Rh­(I) Fischer carbenes, which rearrange through a 1,2-β-hydrogen shift to afford complexes with π-bound product enol ethers. Final substitution of phenylacetylene gives (<i>Z</i>)- and (<i>E</i>)-PhCHCHOMe and regenerates <b>3</b>. The anti-Markovnikov regioselectivity stems from the Rh­(I) vinylidene complex <b>4</b> with reversed C_α and C_β polarity. The stereoselectivity arises from the turnover-limiting transition states (TSs) for the Rh­(I) carbene rearrangement: the <i>Z</i>-product-forming <b>TS24</b> is sterically less congested and hence more stable than the <i>E</i>-product-forming <b>TS25</b>. The difference in energy (1.2 kcal/mol) between <b>TS24</b> and <b>TS25</b> gives a theoretical <i>Z</i> selectivity that agrees well with the experimental value. Calculations were also performed on the key TSs of reactions involving two other alkyne substrates, and the results corroborate the proposed mechanism. The findings taken together give an insight into the roles of the rhodium–quinolinolato chelate framework in directing phenylacetylene attack by trans effect, mediating hydrogen transfers through hydrogen bonding, and differentiating the energies of key TSs by steric repulsion

Genetic Improvement in Juglans mandshurica and Its Uses in China: Current Status and Future Prospects

Juglans mandshurica is an economically and ecologically valuable species that is used for various construction purposes, making luxurious furniture, as food and sources of medicinal substances and landscaping because of its excellent wood, edible fruits and rich in various types of chemical compounds. In the past few decades, several genetic improvements of J. mandshurica were made, with a focus on the selection of improved varieties and on breeding technology. Many elite provenances and families were selected based on growth traits or wood properties. In recent years, with the increasing demand for high-quality seedlings in Chinese forestry production, the breeding goals of genetic improvement for J. mandshurica were redefined to include other traits, such as fruit yield and contents of medicinal component. However, the improvement processes were still slow due to the long breeding cycle and the limited use of advanced breeding technologies, resulting in the selection of fewer improved varieties. In this review, we summarized the research progresses on genetic improvements of J. mandshurica and other related works, and discussed research gaps and suggested future directions for genetic improvement of the species. The review provides valuable insight for the selection of improved varieties and production of excellent germplasms

KCTD10 is involved in the cardiovascular system and Notch signaling during early embryonic development.

As a member of the polymerase delta-interacting protein 1 (PDIP1) gene family, potassium channel tetramerisation domain-containing 10 (KCTD10) interacts with proliferating cell nuclear antigen (PCNA) and polymerase δ, participates in DNA repair, DNA replication and cell-cycle control. In order to further investigate the physiological functions of KCTD10, we generated the KCTD10 knockout mice. The heterozygous KCTD10(+/-) mice were viable and fertile, while the homozygous KCTD10(-/-) mice showed delayed growth from E9.0, and died at approximately E10.5, which displayed severe defects in angiogenesis and heart development. Further study showed that VEGF induced the expression of KCTD10 in a time- and dose-dependent manner. Quantitative real-time PCR and western blotting results revealed that several key members in Notch signaling were up-regulated either in KCTD10-deficient embryos or in KCTD10-silenced HUVECs. Meanwhile, the endogenous immunoprecipitation (IP) analysis showed that KCTD10 interacted with Cullin3 and Notch1 simultaneously, by which mediating Notch1 proteolytic degradation. Our studies suggest that KCTD10 plays crucial roles in embryonic angiogenesis and heart development in mammalians by negatively regulating the Notch signaling pathway

Restriction-based Multiple-fragment Assembly Strategy to Avoid Random Mutation during Long cDNA Cloning

Abstract Long fragment cloning is a challenge for its difficulty in accurate amplifying and tendency to get unwanted mutation. Here we discuss Restriction-based Multiple-fragment Assembly Strategy&apos;s advantages and limitations. In this strategy, rather than PCR amplifying the entire coding sequence (CDS) at one time, we amplified and sequenced smaller fragments which are shorter than 1.5kb spanning the CDS. After that, the sequence-proved fragments were assembled by digestion-ligation cloning to the target vector. We test its universality in our script programmed in Python. Our data shows that, among the entire human and mouse CDS, at least 70% of long CDS cloning will benefit from this strategy