A Critical Residue Selectively Recruits Nucleotides for T7 RNA Polymerase Transcription Fidelity Control

AbstractNucleotide selection is essential for fidelity control in gene replication and transcription. Recent work on T7 RNA polymerase suggested that a small posttranslocation free energy bias stabilizes Tyr639 in the active site to aid nucleotide selection. However, it was not clear exactly how Tyr639 assists the selection. Here we report a molecular-dynamics simulation study revealing atomistic detail of this critical selectivity. The study shows first that Tyr639 blocks the active site at posttranslocation by marginally stacking to the end basepair of the DNA-RNA hybrid. The study then demonstrates that at the nucleotide preinsertion state, a cognate RNA nucleotide does not affect the local Tyr639 stabilization, whereas a noncognate nucleotide substantially stabilizes Tyr639 so that Tyr639 keeps blocking the active site. As a result, further nucleotide insertion into the active site, which requires moving Tyr639 out of the site, would be hindered for the noncognate nucleotide, but not for the cognate nucleotide. In particular, we note that water molecules assist the ribose recognition in the RNA nucleotide preinsertion, and help Tyr639 stacking to the end basepair in the case of a DNA nucleotide. It was also seen that a base-mismatched nucleotide at preinsertion directly grabs Tyr639 for the active site stabilization. We also find that in a mutant polymerase Y639F the strong stabilization of residue 639 in the active site cannot establish upon the DNA nucleotide preinsertion. The finding explains the reduced differentiation between ribo- and deoxyribonucleotides that has been recorded experimentally for the mutant polymerase

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation

Clinical analysis of 1 case of solitary brain metastases misdiagnosed as cerebral infarction

目的  通过报告1例误诊为脑梗死的单发性脑转移瘤患者的诊断过程，总结单发性脑转移瘤的临床、影像学特征及诊断治疗方法。方法  回顾性分析1例单发性脑转移瘤患者的诊断过程，并复习有关文献。结果  脑转移瘤常多发，单发者仅占25%，发病年龄以40～60岁多见，原发病灶以肺最常见。脑转移瘤常位于脑叶灰白质交界处，不同部位的肿瘤可出现不同的临床表现，影像学上常表现为“小病灶、大水肿”，与颅内原发肿瘤不易区分，头颅CT或 MRI增强检查并查到其他部位的原发肿瘤病灶后可确定诊断。目前主张单发性脑转移瘤应进行手术切除，术后辅以立体定向放射治疗和全脑放射治疗。结论  15%的脑转移瘤患者既往无肿瘤病史，因此诊断脑瘤后须在身体其他部位查找有无原发病灶，避免误诊、漏诊。对于中老年肺癌或其他恶性肿瘤患者，无论有无中枢神经系统症状，均应积极进行头颅CT甚至MRI检查，以发现较小的早期脑转移瘤病灶。对于易患肺癌人群，应该每年体检，进行胸部X线检查或低剂量CT筛查，以便早期发现肺癌病灶，早期治疗，防止肿瘤转移。Objective: To report 1 case was misdiagnosed as cerebral infarction solitary brain metastases (SBM) in patients with diagnosis process, and to summarize the clinical and imaging features of the SBM and its treatment. Methods: To retrospectively analyze the diagnostic process of 1 case of SBM patients, and to have literature review. Results: Patients with solitary and multiple brain metastases accounted for only 25%, the onset age was 40 ~ 60 years old, and the most common primary lesion is in lung. Brain metastases are often on the border, in between lobes grey matter. Different parts of the tumors can present different clinical manifestations. The diagnostic imaging is often shown as "small lesions, large edema", and intracranial primary tumor is not easy to distinguish, Head CT or MRI examination of tumors in other parts could confirm the diagnosis. Now that SBM should undergo surgery resection, postoperative supplemented by stereotactic radiotherapy and whole brain radiotherapy. Conclusions: 15% of the patients with brain metastases haven’t got previous medical history, the doctor is therefore must look for presence of primary lesions in other parts of the body for accurate diagnosis, to avoid the misdiagnosis and missed diagnosis. Middle-aged and elderly patients with lung cancer or other malignant tumor, regardless of the presence of the central nervous system symptoms, should carry on the head CT or MRI examination, and find smaller early brain metastatic lesions. People who are susceptible to lung cancer should have annual physical examination, chest X-ray or low dose CT screening for early detection of lung cancer lesions, early treatment and prevention of tumor metastasi

J/psi production from charm coalescence in relativistic heavy ion collisions

J/psi production and collective flow is studied with a coalescence model based on phase space distribution of charm quarks from a multi-phase transport model simulation of relativistic heavy ion collisions. Both the yield and the flow of J/psi particles are sensitive to charm quark final state interactions. As the charm quark rescattering cross section increases from 3 mb to 10 mb, J/psi elliptic flow increases faster than corresponding light hadron elliptic flows. The v_2(p_t) of J/psi crosses that of D mesons to reach a value that is about the peak value of the D meson flow but at a higher p_t. As J/psi elliptic flow has only contributions from charm quarks, it complements D meson elliptic flow in reflecting charm properties in the Quark-Gluon Plasma

Low Cost Seismic Network Practical Applications for Producing Quick Shaking Maps in Taiwan

Two major earthquakes of ML greater than 6.0 occurred in Taiwan in the first half of 2013. The vibrant shaking brought landslides, falling rocks and casualties. This paper presents a seismic network developed by National Taiwan University (NTU) with 401 Micro-Electro Mechanical System (MEMS) accelerators. The network recorded high quality strong motion signals from the two events and produced delicate shaking maps within one minute after the earthquake occurrence. The high shaking regions of the intensity map produced by the NTU system suggest damage and casualty locations. Equipped with a dense array of MEMS accelerometers, the NTU system is able to accommodate 10% signals loss from part of the seismic stations and maintain its normal functions for producing shaking maps. The system also has the potential to identify the rupture direction which is one of the key indices used to estimate possible damage. The low cost MEMS accelerator array shows its potential in real-time earthquake shaking map generation and damage avoidance

Interior regularity criteria for suitable weak solutions of the Navier-Stokes equations

We present new interior regularity criteria for suitable weak solutions of the 3-D Navier-Stokes equations: a suitable weak solution is regular near an interior point $z$ if either the scaled $L^{p,q}_{x,t}$-norm of the velocity with $3/p+2/q\leq 2$, $1\leq q\leq \infty$, or the $L^{p,q}_{x,t}$-norm of the vorticity with $3/p+2/q\leq 3$, $1 \leq q < \infty$, or the $L^{p,q}_{x,t}$-norm of the gradient of the vorticity with $3/p+2/q\leq 4$, $1 \leq q$, $1 \leq p$, is sufficiently small near $z$

An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

<p>Abstract</p> <p>Background</p> <p>Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications – Literature Finder and Investigator Browser – as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources.</p> <p>Results</p> <p>Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective.</p> <p>Conclusion</p> <p>The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.</p

Influence of operational parameters on photocatalytic amitrole degradation using nickel organic xerogel under UV irradiation

The objectives of this study were to analyze the influence of different operational variables and to determine the time course of total organic carbon (TOC) and medium toxicity during amitrole (AMT) photodegradation in the presence of Ni xerogel (X-Ni) as photocatalyst. A further study objective was to analyze the influence of the type of water on the photodegradation process. Results show that the degradation rate is directly proportional to the initial X-Ni concentration up to a maximum of 250 mg/L with a slight decrease thereafter, indicating progressive photon absorption saturation of the catalyst for a given incident radiation flow. At concentrations close to 250 mg/L X-Ni, the AMT photodegradation rate is not affected by further increases in X-Ni concentration. In addition, AMT photolysis is highly pH-dependent and is generally favored at pH values at which AMT is in its ionic form. The increase observed in AMT degradation rate under alkaline conditions can be attributed to the higher generation of radicals. The presence of chloride reduces the AMT degradation rate, because Cl− anions behave as h+ and radical scavengers. The degradation rate is also decreased by addition to the medium of organic matter, which acts as a filter. The behavior of TOC removal kinetics during AMT degradation in the presence of X-Ni is similar to that observed for AMT degradation kinetics. Finally, we highlight that photocatalysis is more effective in ultrapure water than in wastewater or tap water. In all systems, the optimal catalyst concentration is 250 mg/L. The medium toxicity increases with longer treatment time, indicating the formation of by-products that are smaller than AMT and can more readily penetrate the cell.Financial support provided by the Ministerio de Ciencia e Innovación (Spain) and FEDER (Projects CTQ-2011-29035-C02-01 and CTQ-2011-29035- C02-02), and by the University of Jaén (Project UJA 2015/06/01)

cAMP/PKA Regulates Osteogenesis, Adipogenesis and Ratio of RANKL/OPG mRNA Expression in Mesenchymal Stem Cells by Suppressing Leptin

BACKGROUND: Mesenchymal stem cells (MSCs) are a pluripotent cell type that can differentiate into adipocytes, osteoblasts and other cells. The reciprocal relationship between adipogenesis and osteogenesis was previously demonstrated; however, the mechanisms remain largely unknown. METHODS AND FINDINGS: We report that activation of PKA by 3-isobutyl-1 methyl xanthine (IBMX) and forskolin enhances adipogenesis, the gene expression of PPARgamma2 and LPL, and downregulates the gene expression of Runx2 and osteopontin, markers of osteogenesis. PKA activation also decreases the ratio of Receptor Activator of the NF-kappaB Ligand to Osteoprotegerin (RANKL/OPG) gene expression - the key factors of osteoclastogenesis. All these effects are mediated by the cAMP/PKA/CREB pathway by suppressing leptin, and may contribute to PKA stimulators-induced in vivo bone loss in developing zebrafish. CONCLUSIONS: Using MSCs, the center of a newly proposed bone metabolic unit, we identified cAMP/PKA signaling, one of the many signaling pathways that regulate bone homeostasis via controlling cyto-differentiation of MSCs and altering RANKL/OPG gene expression