SiteFinding-PCR: a simple and efficient PCR method for chromosome walking

In this paper, we present a novel PCR method, termed SiteFinding-PCR, for gene or chromosome walking. The PCR was primed by a SiteFinder at a low temperature, and then the target molecules were amplified exponentially with gene-specific and SiteFinder primers, and screened out by another gene-specific primer and a vector primer. However, non-target molecules could not be amplified exponentially owing to the suppression effect of stem–loop structure and could not be screened out. This simple method proved to be efficient, reliable, inexpensive and time-saving, and may be suitable for the molecules for which gene-specific primers are available. More importantly, large DNA fragments can be obtained easily using this method. To demonstrate the feasibility and efficiency of SiteFinding-PCR, we employed this method to do chromosome walking and obtained 16 positive results from 17 samples

Tuber indicum and T. lijiangense colonization differentially regulates plant physiological responses and mycorrhizosphere bacterial community of Castanopsis rockii seedlings

Black truffles and white truffles are widely studied around the world, but their effects on plant growth and physiological responses, and on the mycorrhizosphere bacterial community of the host plant remain unclear. Here, mycorrhizal colonization of Castanopsis rockii by Tuber indicum (Chinese black truffle) and T. lijiangense (Chinese white truffle), respectively, was induced in a greenhouse study, and their effects on host growth, physiological responses and mycorrhizosphere bacterial communities were compared. The results show that colonization of both Tuber species significantly increased leaf photosynthetic rate, leaf P concentration and mycorrhizosphere acid phosphatase activity, as well as richness of mycorrhizosphere bacterial communities of C. rockii seedlings. However, T. indicum colonization on the one hand significantly decreased tartrate content, bacterial acid phosphatase, phoC gene abundance in the mycorrhizosphere, and peroxidase (POD) activity of ectomycorrhizal root tips, but on the other hand increased mycorrhizosphere pH and superoxide dismutase (SOD) of ectomycorrhizal root tips, compared to T. lijiangense colonization. Moreover, principal coordinate and β-diversity analyses show significant differences in mycorrhizosphere bacterial community composition between T. indicum and T. lijiangese colonized C. rockii seedlings. Finally, the relative abundance of the bacterium Agromyces cerinus significantly correlated to mycorrhizosphere acid phosphatase activity and leaf P concentration, suggesting that this bacterium might play an important role in P mobilization and acquisition. Overall, these results suggest that T. indicum and T. lijiangense differently regulate their host plant’s physiological responses and mycorrhizosphere bacterial community

A CAN-BASED P2P INFRASTRUCTURE FOR SEMANTIC WEB SERVICES

(SWS) has received a lot of attention from researchers due to its ability of automatic Web Service discovery, execution and composition. Currently Web Service systems, which publish WSDL-described Web Services in UDDIs, cannot support SWS and UDDI has become the bottleneck of the whole system and would cause single node failure problems. Therefore, we propose a CAN-based P2P system to replace traditional UDDI, by distributing the functions of the UDDI among all the peers in the P2P network. At the same time, we design an ontology-based mechanism, guaranteeing every service would be registered on a specific peer in the CAN-based P2P network, according to the service’s ontology. By replacing the UDDI, our system improves the scalability and stability of the SWS system, and realizes an efficient ontology-based discovery of Semantic Web Services. Key words: Semantic Web Service, P2P network, CAN, Ontology-based discover

The gene mutations and subtelomeric DNA methylation in immunodeficiency, centromeric instability and facial anomalies syndrome

Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disorder, which is characteristic of a severe impairment of immunity. In the genetic aspect, ICF is featured with mutations primarily located in the specific genes (DNMT3B for ICF1, ZBTB24 for ICF2, CDCA7 for ICF3, and HELLS for ICF4). The subtelomeric region is defined as 500 kb at the terminal of each autosomal arm. And subtelomeric DNA fragments can partially regulate key biological activities, including chromosome movement and localization in the nucleus. In this review, we updated and summarized gene mutations in ICF based on the previous review. In addition, we focused on the correlation between subtelomeric DNA methylation and ICF. The relationship between subtelomeric methylation and telomere length in ICF was also summarized

Development and Validation of a Mutational Burden-Associated LncRNA Signature for Improving the Clinical Outcome of Hepatocellular Carcinoma

Background: Long non-coding RNAs (lncRNAs) modulate numerous cellular processes, including DNA damage repair. Here, we investigated the clinical importance of lncRNAs associated with mutational burden in hepatocellular carcinoma (HCC). Methods: Prognosis-related lncRNAs associated with mutational burden were screened and determined to score the mutational burden-associated lncRNA signature (MbLncSig) from TCGA. Prognostic values and predictive performance of the MbLncSig score were analysed. Results: Four mutational burden-associated lncRNAs (AC010643.1, AC116351.1, LUCAT1 and MIR210HG) were identified for establishing the MbLncSig score. The MbLncSig score served as an independent risk factor for HCC prognosis in different subgroup patients. The predictive performance of one-year and three-year OS was 0.739 and 0.689 in the entire cohort, respectively. Moreover, the MbLncSig score can further stratify the patient survival in those with TP53 wild type or mutation. Conclusions: This study identified a four-lncRNA signature (the MbLncSig score) which could predict survival in HCC patient with/without TP53 mutation

ERCC4: a potential regulatory factor in inflammatory bowel disease and inflammation-associated colorectal cancer

The pathogenesis of inflammatory bowel disease (IBD) remains unclear and is associated with an increased risk of developing colitis-associated cancer (CAC). Under sustained inflammatory stimulation in the intestines, loss of early DNA damage response genes can lead to tumor formation. Many proteins are involved in the pathways of DNA damage response and play critical roles in protecting genes from various potential damages that DNA may undergo. ERCC4 is a structure-specific endonuclease that participates in the nucleotide excision repair (NER) pathway. The catalytic site of ERCC4 determines the activity of NER and is an indispensable gene in the NER pathway. ERCC4 may be involved in the imbalanced process of DNA damage and repair in IBD-related inflammation and CAC. This article primarily reviews the function of ERCC4 in the DNA repair pathway and discusses its potential role in the processes of IBD-related inflammation and carcinogenesis. Finally, we explore how this knowledge may open novel avenues for the treatment of IBD and IBD-related cancer

PDGFR inhibition restores morphine efficacy against neuropathic pain.

<p>Animals underwent left L5 SNL as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097105#pone.0097105-Chung1" target="_blank">[11]</a>. Mechanical sensitivity was tested using von Frey filaments and 50% median response threshold determined <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097105#pone.0097105-Dixon1" target="_blank">[13]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097105#pone.0097105-Chaplan1" target="_blank">[14]</a>. Sham operated animals underwent the same surgical procedure except a suture was not tied around the L5 nerve root. (<b>A</b>) Baseline mechanical sensitivity was determined before surgery (BL). Animals then underwent SNL and were allowed to recover for two weeks. Mechanical sensitivity was tested to confirm that SNL induced mechanical allodynia (day 0). SNL animals received daily intrathecal (i.t.) injections of morphine (2 nmol), imatinib (10 µg), or the combination and mechanical sensitivity was determined. Sham operated animals received injections of vehicle alone. Neither morphine nor imatinib alone were analgesic. Co-administration of morphine and imatinib completely reversed SNL-induced mechanical allodynia. n = 8–9 per group. (<b>B</b>) Beginning the day after SNL, animals received daily subcutaneous (s.c.) injections of morphine (2.5 mg/kg), imatinib (5 mg/kg), morphine + imatinib or vehicle and mechanical sensitivity determined. Systemic co-administration of morphine and imatinib completely eliminated allodynia after nerve injury. n = 5–9 per group. (<b>C</b>) Following a two week recovery after SNL, animals received daily i.t. injections of morphine (2 nmol), PDGFR-β-Fc scavenger (500 ng), the combination or vehicle. While PDGFR-β-Fc had no effect on mechanical allodynia, co-administration of morphine and PDGFR-β-Fc completely restored the effectiveness of morphine. n = 7–10 per group. All data presented as grams +/− s.e.m; all p<0.0001 (2-way ANOVA).</p

Mas receptor activation attenuates allergic airway inflammation via inhibiting JNK/CCL2-induced macrophage recruitment

Background: Defective absorption of acute allergic airway inflammation is involved in the initiation and development of chronic asthma. After allergen exposure, there is a rapid recruitment of macrophages around the airways, which promote acute inflammatory responses. The Ang-(1−7)/Mas receptor axis reportedly plays protective roles in various tissue inflammation and remodeling processes in vivo. However, the exact role of Mas receptor and their underlying mechanisms during the pathology of acute allergic airway inflammation remains unclear. Objective: We investigated the role of Mas receptor in acute allergic asthma and explored its underlying mechanisms in vitro, aiming to find critical molecules and signal pathways. Methods: Mas receptor expression was assessed in ovalbumin (OVA)-induced acute asthmatic murine model. Then we estimated the anti-inflammatory role of Mas receptor in vivo and explored expressions of several known inflammatory cytokines as well as phosphorylation levels of MAPK pathways. Mas receptor functions and underlying mechanisms were studied further in the human bronchial epithelial cell line (16HBE). Results: Mas receptor expression decreased in acute allergic airway inflammation. Multiplex immunofluorescence co-localized Mas receptor and EpCAM, indicated that Mas receptor may function in the bronchial epithelium. Activating Mas receptor through AVE0991 significantly alleviated macrophage infiltration in airway inflammation, accompanied with down-regulation of CCL2 and phosphorylation levels of MAPK pathways. Further studies in 16HBE showed that AVE0991 pre-treatment inhibited LPS-induced or anisomycin-induced CCL2 increase and THP-1 macrophages migration via JNK pathways. Conclusion: Our findings suggested that Mas receptor activation significantly attenuated CCL2 dependent macrophage recruitments in acute allergic airway inflammation through JNK pathways, which indicated that Mas receptor, CCL2 and phospho-JNK could be potential targets against allergic airway inflammation