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Identification of bacterial sRNA regulatory targets using ribosome profiling

Bacteria express large numbers of non-coding, regulatory RNAs known as ‘small RNAs’ (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the ...

Morphology and Molecular Mechanisms of Hepatic Injury in Rats under Simulated Weightlessness and the Protective Effects of Resistance Training

citrate, and examined using transmission electron microscopy (TEM) (JEOL1230, JEOL, Tokyo, Japan) according to the method described by Ye Ding [21]. Immunohistochemical assays Primary antibodies used in

Enhanced Performance of Community Health Service Centers during Medical Reforms in Pudong New District of Shanghai, China: A Longitudinal Survey

Background The performance of community health service centers (CHSCs) has not been well monitored and analysed since China’s latest community health reforms in 2009. The aim of the current investigation was to evaluate the performing trends of the CHSCs and to analyze the main factors that could affect the performance in Pudong new district of Shanghai, China. Methods A regional ...

Characterization of the mammalian miRNA turnover landscape

Steady state cellular microRNA (miRNA) levels represent the balance between miRNA biogenesis and turnover. The kinetics and sequence determinants of mammalian miRNA turnover during and after miRNA maturation are not fully understood. Through a large-scale study on mammalian miRNA turnover, we report the co-existence of multiple cellular miRNA pools with distinct turnover kinetics ...

Effects of genetic variations on microRNA: target interactions

Genetic variations within microRNA (miRNA) binding sites can affect miRNA-mediated gene regulation, which may lead to phenotypes and diseases. We perform a transcriptome-scale analysis of genetic variants and miRNA:target interactions identified by CLASH. This analysis reveals that rare variants tend to reside in CDSs, whereas common variants tend to reside in the 3′ UTRs. miRNA ...

On time-domain methods for milling stability analysis

As a basic and advanced machining technique, the high-speed milling process plays an important role in realizing the goal of high performance manufacturing. From the viewpoint of machining dynamics, obtaining chatter-free machining parameters is a prerequisite to guaranteeing machining accuracy and improving machining efficiency. This paper gives an overview on recent progress in ...

Is mammary not otherwise specified-type sarcoma with CD10 expression a distinct entity? A rare case report with immunohistochemical and ultrastructural study

Mammary sarcoma is extremely rare and the diagnosis is established only after metaplastic carcinomas and malignant phyllodes tumours are excluded. A rare case of not otherwise specified-type sarcoma with CD10 expression in the left breast in a 45-year-old female was presented. It was a high-grade tumour composed of spindle cells histologically. The immunohistochemical results ...

STarMir: a web server for prediction of microRNA binding sites

STarMir web server predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA). STarMir is an implementation of logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies (Liu,C., Mallick, B., Long, D., Rennie, W.A., Wolenc, A., Carmack, C.S. and Ding, Y. (2013). CLIP-based prediction of mammalian microRNA ...

The value of Apolipoprotein B/Apolipoprotein A1 ratio for metabolic syndrome diagnosis in a Chinese population: a cross-sectional study

Background The apoB/apoA1 ratio has been reported to be associated with the metabolic syndrome (MetS), and it may be a more convenient biomarker in MetS predicting. However, whether apoB/apoA1 ratio is a better indicator of metabolic syndrome than other biomarkers and what is the optimal cut-off value of apoB/apoA1 ratio as an indicator of metabolic syndrome in Chinese population ...

CLIP-based prediction of mammalian microRNA binding sites

Prediction and validation of microRNA (miRNA) targets are essential for understanding functions of miRNAs in gene regulation. Crosslinking immunoprecipitation (CLIP) allows direct identification of a huge number of Argonaute-bound target sequences that contain miRNA binding sites. By analysing data from CLIP studies, we identified a comprehensive list of sequence, thermodynamic and ...

Grape seed proanthocyanidins ameliorate pancreatic beta-cell dysfunction and death in low-dose streptozotocin- and high-carbohydrate/high-fat diet-induced diabetic rats partially by regulating endoplasmic reticulum stress

Background It is increasingly being realized that failure of pancreatic beta cells to secrete enough insulin to adequately compensate for obesity and insulin resistance is the primary defects of type 2 diabetes mellitus (T2DM). Pancreatic beta cells possess a highly developed and active endoplasmic reticulum (ER), reflecting their role in folding, export and processing of newly ...

Detection of Hepatitis B virus in serum and liver of chickens

Hepatitis B virus (HBV) is one of the most important human pathogens. Its existence in food animals could present a significant threat to public health. The objective of this study was to determine if HBV is present in serum and liver of chickens. A total of 129 serum samples from broiler chickens were collected for the detection of HBV antigens and antibodies, and 193 liver ...

Evaluation of Toxoplasma gondii as a live vaccine vector in susceptible and resistant hosts

Background Toxoplasma gondii has been shown to trigger strong cellular immune responses to heterologous antigens expressed by the parasite in the inbred mouse model 1 . We studied the immune response induced by T. gondii as an effective vaccine vector in chickens and rabbits. Results T. gondii RH strain was engineered to express the yellow fluorescent protein (YFP) in the ...

Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and tested their efficiency in various assays. Using a single directional ligation reaction ...

A statistical sampling algorithm for RNA secondary structure prediction

Ye Ding 0 Charles E. Lawrence 0 0 Bioinformatics Center, Wadsworth Center, New York State Department of Health , 150 New Scotland Avenue, Albany, NY 12208, USA An RNA molecule, particularly a long

Study of Histopathological and Molecular Changes of Rat Kidney under Simulated Weightlessness and Resistance Training Protective Effect

To explore the effects of long-term weightlessness on the renal tissue, we used the two months tail suspension model to simulate microgravity and investigated the simulated microgravity on the renal morphological damages and related molecular mechanisms. The microscopic examination of tissue structure and ultrastructure was carried out for histopathological changes of renal tissue ...

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond

Ye Ding 0 Charles E. Lawrence 0 0 Division of Molecular Medicine, Wadsworth Center, New York State Department of Health , Albany, NY 12201-0509 Single-stranded regions in RNA secondary structure

Structure clustering features on the Sfold Web server

Summary: The energy landscape of RNA secondary structures is often complex, and the Boltzmann-weighted ensemble usually contains distinct clusters. Furthermore, the minimum free energy structure often lies outside of the cluster containing the structure determined by comparative sequence analysis. We have developed procedures to characterize and visualize the Boltzmann-weighted ...

A structural analysis of in vitro catalytic activities of hammerhead ribozymes

Background Ribozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (mRNA) level in both eukaryotic and prokaryotic systems and are thus useful tools for studies of gene function. However, identification of target sites for ...