Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data

MOTIVATION: Discriminant analysis for high-dimensional and low-sample-sized data has become a hot research topic in bioinformatics, mainly motivated by its importance and challenge in applications to tumor classifications for high-dimensional microarray data. Two of the popular methods are the nearest shrunken centroids, also called predictive analysis of microarray (PAM), and shrunken centroids regularized discriminant analysis (SCRDA). Both methods are modifications to the classic linear discriminant analysis (LDA) in two aspects tailored to high-dimensional and low-sample-sized data: one is the regularization of the covariance matrix, and the other is variable selection through shrinkage. In spite of their usefulness, there are potential limitations with each method. The main concern is that both PAM and SCRDA are possibly too extreme: the covariance matrix in the former is restricted to be diagonal while in the latter there is barely any restriction. Based on the biology of gene functions and given the feature of the data, it may be beneficial to estimate the covariance matrix as an intermediate between the two; furthermore, more effective shrinkage schemes may be possible. RESULTS: We propose modified LDA methods to integrate biological knowledge of gene functions (or variable groups) into classification of microarray data. Instead of simply treating all the genes independently or imposing no restriction on the correlations among the genes, we group the genes according to their biological functions extracted from existing biological knowledge or data, and propose regularized covariance estimators that encourages between-group gene independence and within-group gene correlations while maintaining the flexibility of any general covariance structure. Furthermore, we propose a shrinkage scheme on groups of genes that tends to retain or remove a whole group of the genes altogether, in contrast to the standard shrinkage on individual genes. We show that one of the proposed methods performed better than PAM and SCRDA in a simulation study and several real data examples.     

Activity-regulated N-cadherin endocytosis

Enduring forms of synaptic plasticity are thought to require ongoing regulation of adhesion molecules, such as N-cadherin, at synaptic junctions. Little is known about the activity-regulated trafficking of adhesion molecules. Here we demonstrate that surface N-cadherin undergoes a surprisingly high basal rate of internalization. Upon activation of NMDA receptors (NMDAR), the rate of N-cadherin endocytosis is significantly reduced, resulting in an accumulation of N-cadherin in the plasma membrane. Beta-catenin, an N-cadherin binding partner, is a primary regulator of N-cadherin endocytosis. Following NMDAR stimulation, beta-catenin accumulates in spines and exhibits increased binding to N-cadherin. Overexpression of a mutant form of beta-catenin, Y654F, prevents the NMDAR-dependent regulation of N-cadherin internalization, resulting in stabilization of surface N-cadherin molecules. Furthermore, the stabilization of surface N-cadherin blocks NMDAR-dependent synaptic plasticity. These results indicate that NMDAR activity regulates N-cadherin endocytosis, providing a mechanistic link between structural plasticity and persistent changes in synaptic efficacy.     

A new role for cathelicidin in ulcerative colitis in mice

Cathelicidin, an antimicrobial peptide of the innate immune system, modulates microbial growth, wound healing, and inflammation. However, its association with inflammatory bowel diseases (IBDs) is unknown. Our objective was to determine whether cathelicidin would exert a modulatory effect on the progression of IBD and, if so, investigate the mechanism of action through which this effect occurred. We evaluated the potential for a synthetic cathelicidin, the mouse cathelin-related antimicrobial peptide (mCRAMP), to prevent the initiation and promote the healing of lesions from inflammatory colitis that was experimentally induced in mice with dextran sulfate sodium (DSS). During the experiment, mCRAMP was given: (i) as a parallel treatment starting together with 3% DSS feeding, and (ii) as a posttreatment starting 7 days after 3% DSS feeding. The body weight, fecal microflora populations, clinical symptoms, and histologic findings of colonic tissues were measured. Relative gene expression of mucins (MUC1, MUC2, MUC3, and MUC4) in colonic tissues was determined by real-time polymerase chain reaction. Intrarectal administration of mCRAMP ameliorated DSS-induced colitis with negligible effects on mucosal healing. The peptide also significantly reduced the increased number of fecal microflora in colitis animals. It reversed the decline of colonic mucus thickness during colitis through upregulation of the expression of mucin genes. Treatment with mCRAMP also prevented colitis development by suppressing the induction of apoptosis by DSS. The current study demonstrates for the first time that intrarectal administration of cathelicidin may be a novel therapeutic option for IBDs.     

Isolation of New Delhi metallo‐β‐lactamase 1‐producing Vibrio cholerae non‐O1, non‐O139 strain carrying ctxA,st and hly genes in southern Vietnam

Vibrio cholerae non‐O1, non‐O139 (VC_NAG) organisms are universally present in the aquatic environment and regarded as non‐pathogenic bacteria. However, considering that they do occasionally induce gastroenteritis, a study of their virulence and antibiotic resistance genes is important. The presence of enteropathogenic genes, including ctxA, VC_NAG‐specific heat‐stable toxin gene (st), hemolysin (hly), and zona occludens toxin (zot) was determined by PCR in 100 VC_NAG strains isolated in southern Vietnam in 2010–2013 from 94 environmental and six human origins. These 100 VC_NAG strains were also tested phenotypically and genotypically for the presence of the New Delhi metallo‐β‐lactamase (NDM‐1). Of the 100 VC_NAG strains tested, six were positive for ctxA; five from the environment and one of human origin. The st gene was detected in 17 isolates, 15 and two of which were of environmental and human origins, respectively. Gene hly was detected in 19 VC_NAG strains examined, two of which were isolated from humans and 17 from environments. The zot gene was not detected in any of the strains tested. Three VC_NAG strains of environmental origin were confirmed to produce NDM‐1 and the bla_NDM‐1 gene was detected in those strains by PCR. Of note, one of the three NDM‐1‐producing VC_NAG strains was confirmed to carry ctxA, st and hly genes concurrently. This is the first report of isolation of NDM‐1‐producing VC_NAG strains in Vietnam.     

黑龙江省一株红小豆锈病病原菌鉴定

【目的】为明确发生在黑龙江省大庆市红小豆田中的锈病病原物的分类地位。【方法】从大庆市采集红小豆锈病标样,采用单孢子堆分离法获得一株红小豆锈病菌纯培养物ZXL01。采用观测夏孢子芽孔数目、位置和冬孢子壁厚度等形态学特征结合ITS序列分析的方法,对其进行鉴定。【结果】ZXL01夏孢子发芽孔多为2个,位于孢子赤道部位较远之处,冬孢子壁厚度为2.9μm-3.3μm。在基于r DNA-ITS序列构建的系统发育树中,ZXL01菌株与两株豇豆单胞锈菌(Uromyces vignae)的参比菌株(Gen Bank登录号:AB115718和AB115731)在自举值99%相聚一群。用豇豆单胞锈菌的特异性引物UV-ITSF/R进行检测,ZXL01菌株可扩增出500 bp左右的特征片段。【结论】黑龙江省大庆市红小豆锈病病原菌ZXL01菌株为豇豆单胞锈菌,ZXL01菌株的Gen Bank登录号是KM461700。     

Exposure to serotonin adversely affects oligodendrocyte development and myelination in vitro

Serotonin (5‐hydroxytryptamine, 5‐HT) has been implicated to play critical roles in early neural development. Recent reports have suggested that perinatal exposure to selective serotonin reuptake inhibitors (SSRIs) resulted in cortical network miswiring, abnormal social behavior, callosal myelin malformation, as well as oligodendrocyte (OL) pathology in rats. To gain further insight into the cellular and molecular mechanisms underlying SSRIs‐induced OL and myelin abnormalities, we investigated the effect of 5‐HT exposure on OL development, cell death, and myelination in cell culture models. First, we showed that 5‐HT receptor 1A and 2A subtypes were expressed in OL lineages, using immunocytochemistry, Western blot, as well as intracellular Ca²⁺ measurement. We then assessed the effect of serotonin exposure on the lineage development, expression of myelin proteins, cell death, and myelination, in purified OL and neuron‐OL myelination cultures. For pure OL cultures, our results showed that 5‐HT exposure led to disturbance of OL development, as indicated by aberrant process outgrowth and reduced myelin proteins expression. At higher doses, such exposure triggered a development‐dependent cell death, as immature OLs exhibited increasing susceptibility to 5‐HT treatment compared to OL progenitor cells (OPC). We showed further that 5‐HT‐induced immature OL death was mediated at least partially via 5‐HT2A receptor, since cell death could be mimicked by 5‐HT2A receptor agonist 1‐(2,5‐dimethoxy‐4‐iodophenyl)‐2‐aminopropane hydrochloride, (±)‐2,5‐dimethoxy‐4‐iodoamphetamine hydrochloride, but atten‐uated by pre‐treatment with 5‐HT2A receptor antagonist ritanserin. Utilizing a neuron‐OL myelination co‐culture model, our data showed that 5‐HT exposure significantly reduced the number of myelinated internodes. In contrast to cell injury observed in pure OL cultures, 5‐HT exposure did not lead to OL death or reduced OL density in neuron‐OL co‐cultures. However, abnormal patterns of contactin‐associated protein (Caspr) clustering were observed at the sites of Node of Ranvier, suggesting that 5‐HT exposure may affect other axon‐derived factors for myelination. In summary, this is the first study to demonstrate that manipulation of serotonin levels affects OL development and myelination, which may contribute to altered neural connectivity noted in SSRIs‐treated animals.