Identification of differentially expressed genes in primary Sjögren's syndrome

Primary Sjögren's syndrome (pSS) is a chronic systemic autoimmune disease that affects exocrine glands. To study the molecular mechanism and identify crucial genes/pathways in pSS pathogenesis, the microarray-based whole-genome gene expression profiles from salivary glands of patients with pSS and non-sicca controls were retrieved. After normalization and subsequent batch effect adjustment, significance analysis of microarrays method was applied to five available datasets, and 379 differentially expressed genes (DEGs) were identified. The 300 upregulated DEGs were enriched in Gene Ontology terms of immune and inflammatory responses, including antigen processing and presentation, interferon-mediated signaling pathway, and chemotaxis. Previously reported pSS-associated genes, including HLA-DRA, TAP2, PRDM1, and IFI16, were found to be significantly upregulated. The downregulated DEGs were enriched in pathways of salivary secretion, carbohydrate digestion and absorption, and starch and sucrose metabolism, implying dysfunction of salivary glands during pathogenesis. Next, a protein-protein interaction network was constructed, and B2M, an upregulated DEG, was shown to be a hub, suggesting its potential involvement in pSS development. In summary, we found the activation of pSS-associated genes in pathogenesis, and provide clues for salivary glands dysfunction. Experimental investigation on the identified DEGs in this study will deepen our understanding on pSS.     

Accurate,Fully-Automated NMR Spectral Profiling for Metabolomics

Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites) that appear in a person’s biofluids, which means such diseases can often be readily detected from a person’s “metabolic profile"—i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR) spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person’s metabolic profile. Given a 1D ¹H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid), BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the “signatures” of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF), defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error), in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively—with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. BAYESIL is accessible at http://www.bayesil.ca.     

Silibinin ameliorates Aβ<Subscript>25-35</Subscript>-induced memory deficits in rats by modulating autophagy and attenuating neuroinflammation as well as oxidative stress

Alzheimer’s disease (AD) is a progressive, neurodegenerative disease. Accumulating evidence suggests that inflammatory response, oxidative stress and autophagy are involved in amyloid β (Aβ)-induced memory deficits. Silibinin (silybin), a flavonoid derived from the herb milk thistle, is well known for its hepatoprotective activities. In this study, we investigated the neuroprotective effect of silibinin on Aβ_25-35-injected rats. Results demonstrated that silibinin significantly attenuated Aβ_25-35-induced memory deficits in Morris water maze and novel object-recognition tests. Silibinin exerted anxiolytic effect in Aβ_25-35-injected rats as determined in elevated plus maze test. Silibinin attenuated the inflammatory responses, increased glutathione (GSH) levels and decreased malondialdehyde (MDA) levels, and upregulated autophagy levels in the Aβ_25-35-injected rats. In conclusion, silibinin is a potential candidate for AD treatment because of its anti-inflammatory, antioxidant and autophagy regulating activities.     

The Raf-like kinase Raf36 negatively regulates plant resistance against the oomycete pathogen Phytophthora parasitica by targeting MKK2

Oomycetes represent a unique group of plant pathogens that are phylogenetically distant from true fungi and cause significant crop losses and environmental damage. Understanding of the genetic basis of host plant susceptibility facilitates the development of novel disease resistance strategies. In this study, we report the identification of an Arabidopsis thaliana T-DNA mutant with enhanced resistance to Phytophthora parasitica with an insertion in the Raf-like mitogen-activated protein kinase kinase kinase gene Raf36. We generated additional raf36 mutants by CRISPR/Cas9 technology as well as Raf36 complementation and overexpression transformants, with consistent results of infection assays showing that Raf36 mediates Arabidopsis susceptibility to P. parasitica. Using a virus-induced gene silencing assay, we silenced Raf36 homologous genes in Nicotiana benthamiana and demonstrated by infection assays the conserved immune function of Raf36. Mutagenesis analyses indicated that the kinase activity of Raf36 is important for its immune function and interaction with MKK2, a MAPK kinase. By generating and analysing mkk2 mutants and MKK2 complementation and overexpression transformants, we found that MKK2 is a positive immune regulator in the response to P. parasitica infection. Furthermore, infection assay on mkk2 raf36 double mutant plants indicated that MKK2 is required for the raf36-conferred resistance to P. parasitica. Taken together, we identified a Raf-like kinase Raf36 as a novel plant susceptibility factor that functions upstream of MKK2 and directly targets it to negatively regulate plant resistance to P. parasitica.     

七种云南地衣植物的化学成分

本文报道分属于三个科的七种云南产地衣植物的化学成分。这些植物是亚洲树发(Alectoria asiatica DR.)、沟树发(Alectoria sulcata Nyl.)、长茎松萝(Usnea longissimaAch.)、胡子松萝(Usnea comosa(Ach.)Rohl.)、林石蕊(Cladonia arbuscula(Rabh.)Rabh.)、砖孢发(Oropogon loxensis(Fee.)Th.Fr.)和卷梢雪花衣(Anaptychiaboryi(Fee.)Mass.)。根据光谱数据测定,其化学成分为:松萝酸(Usnic acid)(1),维任西酸(Virensic acid)(2),赤星衣酸乙酯(Ethyl haematommate)(3),瑞藏酸(Rhizonic acid)(4),赤星衣酸(Haematommic acid)(5),扁枝衣酸乙酯(Ethyleverninate)(6),黑茶渍素(Atranorin)(7)和泽屋萜(Zeorin)(8)。上述资料,对开发利用这些植物资源提供了科学依据。     

Aging-associated reductions in AMP-activated protein kinase activity and mitochondrial biogenesis

Recent studies have demonstrated a strong relationship between aging-associated reductions in mitochondrial function, dysregulated intracellular lipid metabolism, and insulin resistance. Given the important role of the AMP-activated protein kinase (AMPK) in the regulation of fat oxidation and mitochondrial biogenesis, we examined AMPK activity in young and old rats and found that acute stimulation of AMPK-alpha(2) activity by 5'-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside (AICAR) and exercise was blunted in skeletal muscle of old rats. Furthermore, mitochondrial biogenesis in response to chronic activation of AMPK with beta-guanidinopropionic acid (beta-GPA) feeding was also diminished in old rats. These results suggest that aging-associated reductions in AMPK activity may be an important contributing factor in the reduced mitochondrial function and dysregulated intracellular lipid metabolism associated with aging.     

基于VAR模型的森林植被碳储量影响因素分析——以陕西省为例

森林作为陆地生态系统最大的碳库,对现在及未来的气候变化、碳平衡都具有重要影响。而对影响森林植被碳库的自然和非自然因素进行研究更是对增强森林的碳汇作用,继而改善生态环境状况意义重大。现有的森林动态模型虽然可以很好的模拟碳储量各影响因子之间的联系,但研究往往集中于小尺度从单一影响因素着手,且由于确定模型输入变量和参数的复杂性,使得这些模型在区域甚至更大尺度上的应用存在着一些困难。因此,运用VAR模型,以陕西省为例,构建森林植被碳储量与病虫害发生面积、木材产量、森林火灾面积、森林抚育面积、人工更新造林面积、降水和温度之间的动态关系,来验证该模型在省级尺度条件下的区域森林植被碳储量影响因素分析中的可行性。结果表明:各变量在5%的显著性水平下呈一阶单整序列并具有长期稳定的均衡关系,VAR模型也通过了平稳性检验满足运行的前提条件。通过脉冲响应和方差分解分析可知,森林病虫害、木材产量对陕西省森林植被碳储量呈现出很明显的负作用,并且贡献度很高,分别为5.61%和4.52%;森林抚育、人工更新造林对碳储量的影响存在一定的滞后期;火灾、温度和降水的冲击给碳储量带来的影响均不明显。模型较好的模拟了各影响因素对陕西省碳储量的影响,且具有一定的现实意义,因此,该模型可应用于省级尺度条件下的区域森林植被碳储量影响因素分析。