Suitability of Mycorrhiza-Defective Rice and Its Progenitor for Studies on the Control of Nitrogen Loss in Paddy Fields via Arbuscular Mycorrhiza

Employing mycorrhiza-defective mutants and their progenitors does not require inoculation or elimination of the resident microbial community in the experimental study of mycorrhizal soil ecology. We aimed to examine the suitability of mycorrhiza-defective rice (non-mycorrhizal, Oryza sativa L., cv. Nipponbare) and its progenitor (mycorrhizal) to evaluate nitrogen (N) loss control from paddy fields via arbuscular mycorrhizal (AM) fungi. We grew the two rice lines in soils with the full community of AM fungi and investigated root AM colonization. In the absence of AM fungi, we estimated rice N content, soil N concentration and microbial community on the basis of phospholipid fatty acids; we also quantified N loss via NH3 volatilization, N2O emission, runoff and leaching. In the presence of AM fungi, we did not find any evidence of AM colonization for non-mycorrhizal rice while mycorrhizal rice was colonized and percentage of root colonization was 17–24%. In the absence of AM fungi, the two rice lines had similar N content, soil N concentration and microbial community. Importantly, there was no significant difference in N loss via all the four pathways between mycorrhizal and non-mycorrhizal systems. This mycorrhizal/non-mycorrhizal rice pair is suitable for further research on the role of AM fungi in the control of soil N loss in paddy fields

Therapeutic Discovery for Friedreich Ataxia Using Random shRNA Selection

We screened a 300,000-clone, random shRNA-expressing library and identified shRNA sequences that reverse the decreased growth/survival phenotype of primary Friedreich ataxia (FA) fibroblasts grown in mitochondrial stress media. One of the hit sequences, gFA2, increases frataxin expression ~2 fold, either as a vector-expressed shRNA or as a transfected siRNA. We randomly mutagenized gFA2 to create a gFA2 variant sub-library. We screened this sub-library in primary FA fibroblasts and identified two gFA2 variants, gFA2.8 and gFA2.10, that further increase frataxin expression. Microarray analyses of primary FA fibroblasts expressing another hit shRNA, gFA11, revealed alterations in ~350 mRNAs. Bioinformatic pathway analyses indicated significant changes in mRNAs involved in cytokine secretion; we confirmed significant changes in cytokine secretion induced by gFA11 biochemically. Ingenuity Pathway Analysis revealed that inhibition of a known transcription factor, or treatment of cells with a previously studied chemical compound, induced a statistically similar pattern of gene expression to that induced by gFA11. Inhibition of the transcription factor using a directed siRNA in primary FA fibroblasts, as well as treatment of the cells with the chemical compound, recapitulated the phenotype induced by gFA11, namely reversal of decreased growth/survival in mitochondrial stress media. We are currently planning similar microarray and bioinformatics analyses of the optimized versions of gFA2. Combined with microarray analyses and bioinformatic pattern-matching, our random, shRNA library screens potentially yield, 1) small-RNA therapeutic candidates, 2) conventional chemical-compound therapeutic candidates, 3) drug-target candidates, and 4) elucidation of disease mechanisms, which may inform additional therapeutic initiatives

Identification of p38 MAPK as a novel therapeutic target for Friedreich\u27s ataxia.

Friedreich ataxia (FRDA) is an autosomal recessive neuro- and cardio-degenerative disorder caused by decreased expression of frataxin, a protein that localizes to mitochondria and is critical for iron-sulfur-cluster (ISC) assembly. There are no proven effective treatments for FRDA. We previously screened a random shRNA library and identified a synthetic shRNA (gFA11) that reverses the growth defect of FRDA cells in culture. We now report that gFA11 decreases cytokine secretion in primary FRDA fibroblasts and reverts other changes associated with cell senescence. The gene-expression profile induced by gFA11 is remarkably similar to the gene-expression profile induced by the p38 MAPK inhibitor SB203580. We found that p38 phosphorylation, indicating activation of the p38 pathway, is higher in FRDA cells than in normal control cells, and that siRNA knockdown of frataxin in normal fibroblasts also increases p38 phosphorylation. Treatment of FRDA cells with p38 inhibitors recapitulates the reversal of the slow-growth phenotype induced by clone gFA11. These data highlight the involvement of the p38 MAPK pathway in the pathogenesis of FRDA and the potential use of p38 inhibitors as a treatment for FRDA

Effect of Pomegranate Juice on Dextran Sulfate Sodium Salt-Induced Ulcerative Colitis in Mice

Ulcerative colitis is a chronic inflammatory bowel disease with unclear pathogenesis and is difficult to cure. The incidence rate is increasing year by year, and there is high drug dependence for the treatment of ulcerative colitis, which leads to obvious the treatment resistance to s side effects. Therefore, seeking natural health products for nutritional therapy has become an attention focus of attention. In this articlestudy, dextran sulfate sodium salt (DSS) was used to establish a mouse model of ulcerative colitis. The mice were intervened with 5-aminosalicylic acid (5-ASA) (130 mg/(kg mb∙d)) or pomegranate juice (30% and 100%, 10 mL/d). Body mass, disease activity index (DAI) and colon length were measured, liver and kidney function and oxidative stress were measured by biochemical kits, the levels of inflammatory factors were measured by enzyme-linked immunosorbent assay (ELISA), colon tissue sections were observed, and the contents of fecal short-chain fatty acids (SCFAs) were determined by gas chromatography-mass spectrometry (GC-MS). Finally, a comprehensive evaluation of the effect and mechanism of pomegranate juice against ulcerative colitis in mice was exploredperformed. Compared with the DSS group, body mass and colon length in the pomegranate juice intervention group was increased, DAI was decreased, liver and kidney functions were improved, and could the expression of proinflammatory factors was significantly decreased (P < 0.01). In addition, anti-inflammatory factor expression was significantly enhanced (P < 0.01), reduce the level of oxidative stress and the activity of inflammatory marker myeloperoxidase (MPO) were significantly reduced (P < 0.01), the level of up-regulate fecal SCFAs was up-regulated, andimprove the colonic epithelial structure was improved. Pomegranate juice can attenuate intestinal mucosal damage and liver and kidney dysfunction, and has a good therapeutic effect on DSS-induced ulcerative colitis in mice

Antisaccadic eye movements in middle-aged individuals with a family history of Alzheimer's disease

BackgroundAntisaccade is closely associated with cognitive ability in Alzheimer's disease (AD). However, studies regarding antisaccade in the early stages of AD are scarce. Considering that first-degree family history is a well-established risk factor for AD, we explored the influence of family history on the performance of antisaccade tasks in individuals with normal cognition.MethodsIn total, 44 participants (aged 50–66 years) with a family history of AD (FH+) and 44 age-, gender-, and educational level-matched controls (FH-) were enrolled in our study. After cognitive assessment using the Montreal Cognitive Assessment and Mini-mental State Examination, participants underwent antisaccade trials, and all parameters were recorded using an eye tracker.ResultsWhile the average velocity was relatively lower in FH+ individuals than in FH− individuals (107.9 ± 14.3°/s vs. 132.9 ± 23.7°/s, p &lt; 0.001), FH+ individuals surprisingly showed relatively fewer uninhibited reflexive saccades (44.7 ± 26.0% vs. 56.2 ± 24.7%, p = 0.037) than the control group. They also required a relatively shorter time to detect and correct false saccades (121.6 ± 40.7 ms vs. 143.9 ± 37.0 ms, p = 0.023).ConclusionsThis study showed that family history is associated with alterations in antisaccadic parameters, suggesting that eye tracking can be used to assess oculomotor control and executive function in individuals at risk of developing dementia

Mechanism of Lactiplantibacillus plantarum regulating Ca2+ affecting the replication of PEDV in small intestinal epithelial cells

Porcine epidemic diarrhea virus (PEDV) mainly invades the small intestine and promotes an inflammatory response, eventually leading to severe diarrhea, vomiting, dehydration, and even death of piglets, which seriously threatens the economic development of pig farming. In recent years, researchers have found that probiotics can improve the intestinal microenvironment and reduce diarrhea. At the same time, certain probiotics have been shown to have antiviral effects; however, their mechanisms are different. Herein, we aimed to investigate the inhibitory effect of Lactiplantibacillus plantarum supernatant (LP-1S) on PEDV and its mechanism. We used IPEC-J2 cells as a model to assess the inhibitory effect of LP-1S on PEDV and to further investigate the relationship between LP-1S, Ca2+, and PEDV. The results showed that a divalent cation chelating agent (EGTA) and calcium channel inhibitors (Bepridil hydrochloride and BAPTA-acetoxymethylate) could inhibit PEDV proliferation while effectively reducing the intracellular Ca2+ concentration. Furthermore, LP-1S could reduce PEDV-induced loss of calcium channel proteins (TRPV6 and PMCA1b), alleviate intracellular Ca2+ accumulation caused by PEDV infection, and promote the balance of intra- and extracellular Ca2+ concentrations, thereby inhibiting PEDV proliferation. In summary, we found that LP-1S has potential therapeutic value against PEDV, which is realized by modulating Ca2+. This provides a potential new drug to treat PEDV infection

Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

BACKGROUND: Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. METHODOLOGY/PRINCIPAL FINDINGS: Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R(2) methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. CONCLUSIONS: By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study

Cassava genome from a wild ancestor to cultivated varieties

Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology