Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, messages are carried by neurotransmitters released from presynaptic terminals and received by receptors on postsynaptic cells. Our previous research in Caenorhabditis elegans has shown that VSM-1 negatively regulates exocytosis. Additionally, analysis of synapses in vsm-1 mutants showed that animals lacking a fully functional VSM-1 have increased synaptic connectivity. Based on these preliminary findings, we hypothesized that C. elegans VSM-1 may play a crucial role in synaptogenesis. To test this hypothesis, double-labeled microarray analysis was performed, and gene expression profiles were determined. First, total RNA was isolated, reversely transcribed to cDNA, and hybridized to the DNA microarrays. Then, in-silico analysis of fluorescent probe hybridization revealed significant induction of many genes coding for members of the major sperm protein family (MSP) in mutants with enhanced synaptogenesis. MSPs are the major component of sperm in C. elegans and appear to signal nematode oocyte maturation and ovulation . In fruit flies, Chai and colleagues ¹ demonstrated that MSP-like molecules regulate presynaptic bouton number and size at the neuromuscular junction. Moreover, analysis performed by Tsuda and coworkers ² suggested that MSPs may act as ligands for Eph receptors and trigger receptor tyrosine kinase signaling cascades. Lastly, real time PCR analysis corroborated that the gene coding for MSP-32 is induced in vsm-1(ok1468) mutants. Taken together, research performed by our laboratory has shown that vsm-1 mutants have a significant increase in synaptic density, which could be mediated by MSP-32 signaling.     

Microarray Multiplex Assay for the Simultaneous Detection and Discrimination of Influenza A and Influenza B Viruses

In this study, we present a microarray approach for the typing of influenza A and B viruses, and the subtyping of H1 and H3 subtypes. We designed four pairs of specific multiplex RT-PCR primers and eight specific oligonucleotide probes and prepared microarrays to identify the specific subtype of influenza virus. Through amplification and fluorescent marking of the multiplex RT-PCR products on the M gene of influenza A and B viruses and the HA gene of subtypes H1 and H3, the PCR products were hybridized with the microarray, and the results were analyzed using a microarray scanner. The results demonstrate that the chip developed by our research institute can detect influenza A and B viruses specifically and identify the subtypes H1 and H3 at a minimum concentration of 1 × 10² copies/μL of viral RNA. We tested 35 clinical samples and our results were identical to other fluorescent methods. The microarray approach developed in this study provides a reliable method for the monitoring and testing of seasonal influenza.     

Profiles of Serum Cytokines in Acute Drug-Induced Liver Injury and Their Prognostic Significance

Drug-induced liver injury (DILI) is the most common cause of acute liver failure in the United-States. The aim of the study was to describe serum immune profiles associated with acute DILI, to investigate whether there are profiles associated with clinical features or types of DILI and/or with prognosis, and to assess temporal changes in levels. Twenty-seven immune analytes were measured in the sera of 78 DILI subjects in the Drug-Induced Liver Injury Network (DILIN) and compared with 40 healthy controls. Immune analytes (14 cytokines, 7 chemokines and 6 growth factors) were measured by BioPlex multiplex ELISA at DILI onset and after 6 months. A modeling process utilizing immune principles was used to select a final set of variables among 27 immune analytes and several additional clinical lab values for prediction of early death (within 6 months of DILI onset). Nineteen of the 27 immune analytes were differentially expressed among healthy control, DILI onset and 6-month cohorts. Disparate patterns of immune responses, especially innate and adaptive cellular (mostly TH17) immunity were evident. Low values of four immune analytes (IL-9, IL-17, PDGF-bb and RANTES) and serum albumin are predictive of early death [PPV = 88% (95% CI, 65%-100%), NPV = 97% (95% CI, 93%-100%), accuracy = 96% (95% CI, 92%-100%)].

Conclusions

Acute DILI is associated with robust and varying immune responses. High levels of expression of cytokines associated with innate immunity are associated with a poor prognosis, whereas high levels of expression of adaptive cytokines are associated with good long-term prognosis and eventual recovery. Serum immune analyte profiles at DILI onset appear to be of prognostic, and perhaps, diagnostic significance.     

基因表达谱中信号通路基因集分析方法进展

微阵列技术是生物技术变革的核心,允许研究者同时监测成千上万个基的表达水平,已广泛应用医学研究.如何挖掘海量基表达信息中的有用信息并进行生物学专业解释,是基表达谱数据分析领所面临的一个重要挑战.生物信号通路研究已成为基芯片中不同表型差异表达研究的主要方法,其是以整个信号通路作为一个整体作为研究对象,此得出的研究结果更加科学和准确.在本文中我们简要描述了近10年来信号通路基集富集分析方法的发展情况,将其分为三个阶段,对每个阶段方法的基础和特点做了一些简单的总结和阐述.     

Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray. We used the microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array- and sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Finally, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.     

首次从啮齿类和食虫类动物中分离到森林脑炎病毒

1988年,我们从采自云南高黎贡山的卵形硬蜱及患者血液中分离到森林脑炎病毒。1990年,又从该地区10种95只啮齿类中查到森林脑炎病毒抗体;并从社鼠(R.confucianus)、小林姬鼠(A.sylvaticus)和灰腹鼠(R.eha ninus)等8种啮齿类及食虫类中分离到15株病毒,选三株用单克隆抗体进行免疫荧光试验、理化特性、生物学特性及中和试验研究。结果表明,其病毒的抗原性、生物学特性及理化特性与东北株及从卵形硬蜱、患者分离的森林脑炎病毒一致。从啮齿类及食虫类分离到森林脑炎病毒在国内属首次报道。这项研究结果进一步证明,啮食类和食虫类在森林脑炎自然疫源地的保存方面起重要作用。     

绝经对血液单核细胞基因表达谱的影响:基因芯片初步研究

绝经是女性一生中很重要的生理现象之一,它能增加一系列复杂免疫、神经退化、新陈代谢和心血管方面的疾病。血液单核细胞能分化成各种各样的细胞,这些细胞在组织形态发生和免疫应答方面起着很重要的作用。本研究中采用了包含大约14,500个基因探针的Affymetrix Human U133A基因芯片来研究健康的绝经前和绝经后女性外周血液单核细胞中的基因表达谱。样本之间的对比分析表明有20个基因上调,20个基因下调。其中的28个基因根据它们的生物过程如细胞繁殖、免疫应答、细胞代谢等等被分成了6个主要的GO类别;剩下的12个基因其生物学功能还没有被鉴定。研究结果支持了我们的假设:血液单核细胞的功能状态确实受到绝经的影响,而且由此带来的改变可能是由全基因组范围的基因表达谱而决定的。本研究中鉴定的一些差异表达基因有可能作为以后研究与绝经相关的系统免疫、神经退化和心血管疾病的候选基因研究。此工作是这个研究方向的第一次尝试,为将来的进一步研究奠定了基础。     

采用基因微阵列技术对常见呼吸道病毒进行检测的初步研究

建立一种高通量的基因微阵列检测技术,对常见呼吸道病毒感染进行监控.根据公开发表的8个病毒科38种常见呼吸道病毒的序列,计算其保守区域,设计病毒的特异性检测探针,制备呼吸道病毒检测基因微阵列.利用随机引物PCR方法标记样品中的病毒靶序列,标记产物与基因微阵列上的探针杂交,清洗、扫描后进行结果分析.采用流感病毒、麻疹病毒、腮腺炎病毒和风疹病毒作为报告病毒,并对80例上呼吸道感染患者的咽拭子标本进行验证测试.初步结果表明,该呼吸道病毒微阵列基因芯片检测是可行的,在利用基因微阵列技术对病毒监控方面进行了有益的尝试,得到了有经验的信息.     

DNA Methylation Profiles and Their Relationship with Cytogenetic Status in Adult Acute Myeloid Leukemia

Background

Aberrant promoter DNA methylation has been shown to play a role in acute myeloid leukemia (AML) pathophysiology. However, further studies to discuss the prognostic value and the relationship of the epigenetic signatures with defined genomic rearrangements in acute myeloid leukemia are required.

Methodology/Principal Findings

We carried out high-throughput methylation profiling on 116 de novo AML cases and we validated the significant biomarkers in an independent cohort of 244 AML cases. Methylation signatures were associated with the presence of a specific cytogenetic status. In normal karyotype cases, aberrant methylation of the promoter of DBC1 was validated as a predictor of the disease-free and overall survival. Furthermore, DBC1 expression was significantly silenced in the aberrantly methylated samples. Patients with chromosome rearrangements showed distinct methylation signatures. To establish the role of fusion proteins in the epigenetic profiles, 20 additional samples of human hematopoietic stem/progenitor cells (HSPC) transduced with common fusion genes were studied and compared with patient samples carrying the same rearrangements. The presence of MLL rearrangements in HSPC induced the methylation profile observed in the MLL-positive primary samples. In contrast, fusion genes such as AML1/ETO or CBFB/MYH11 failed to reproduce the epigenetic signature observed in the patients.

Conclusions/Significance

Our study provides a comprehensive epigenetic profiling of AML, identifies new clinical markers for cases with a normal karyotype, and reveals relevant biological information related to the role of fusion proteins on the methylation signature.     

Microarray Analysis of Gene Expression Profiles of Schistosoma japonicum Derived from Less-Susceptible Host Water Buffalo and Susceptible Host Goat

Background

Water buffalo and goats are natural hosts for S. japonicum in endemic areas of China. The susceptibility of these two hosts to schistosome infection is different, as water buffalo are less conducive to S. japonicum growth and development. To identify genes that may affect schistosome development and survival, we compared gene expression profiles of schistosomes derived from these two natural hosts using high-throughput microarray technology.

Results

The worm recovery rate was lower and the length and width of worms from water buffalo were smaller compared to those from goats following S. japonicum infection for 7 weeks. Besides obvious morphological difference between the schistosomes derived from the two hosts, differences were also observed by scanning and transmission electron microscopy. Microarray analysis showed differentially expressed gene patterns for parasites from the two hosts, which revealed that genes related to lipid and nucleotide metabolism, as well as protein folding, sorting, and degradation were upregulated, while others associated with signal transduction, endocrine function, development, immune function, endocytosis, and amino acid/carbohydrate/glycan metabolism were downregulated in schistosomes from water buffalo. KEGG pathway analysis deduced that the differentially expressed genes mainly involved lipid metabolism, the MAPK and ErbB signaling pathways, progesterone-mediated oocyte maturation, dorso-ventral axis formation, reproduction, and endocytosis, etc.

Conclusion

The microarray gene analysis in schistosomes derived from water buffalo and goats provide a useful platform to disclose differences determining S. japonicum host compatibility to better understand the interplay between natural hosts and parasites, and identify schistosome target genes associated with susceptibility to screen vaccine candidates.     

Comparative Spatial Dynamics of Japanese Encephalitis and Acute Encephalitis Syndrome in Nepal

Japanese Encephalitis (JE) is a vector-borne disease of major importance in Asia. Recent increases in cases have spawned the development of more stringent JE surveillance. Due to the difficulty of making a clinical diagnosis, increased tracking of common symptoms associated with JE—generally classified as the umbrella term, acute encephalitis syndrome (AES) has been developed in many countries. In Nepal, there is some debate as to what AES cases are, and how JE risk factors relate to AES risk. Three parts of this analysis included investigating the temporal pattern of cases, examining the age and vaccination status patterns among AES surveillance data, and then focusing on spatial patterns of risk factors. AES and JE cases from 2007–2011 reported at a district level (n = 75) were examined in relation to landscape risk factors. Landscape pattern indices were used to quantify landscape patterns associated with JE risk. The relative spatial distribution of landscape risk factors were compared using geographically weighted regression. Pattern indices describing the amount of irrigated land edge density and the degree of landscape mixing for irrigated areas were positively associated with JE and AES, while fragmented forest measured by the number of forest patches were negatively associated with AES and JE. For both JE and AES, the local GWR models outperformed global models, indicating spatial heterogeneity in risks. Temporally, the patterns of JE and AES risk were almost identical; suggesting the relative higher caseload of AES compared to JE could provide a valuable early-warning signal for JE surveillance and reduce diagnostic testing costs. Overall, the landscape variables associated with a high degree of landscape mixing and small scale irrigated agriculture were positively linked to JE and AES risk, highlighting the importance of integrating land management policies, disease prevention strategies and promoting healthy sustainable livelihoods in both rural and urban-fringe developing areas.     

Semantic Profiles of Zoos and Their Animals

ABSTRACT

I administered surveys to 156 university students to explore issues related to animal charisma or show value. Specifically, students ranked species as to their desirability to see on a zoo tour and to work with professionally as a zoo biologist; rated the semantic connotations of these species; rated the semantic connotations of the zoo, wild animal park, and nature reserve; and rated the connotations of two charismatic and two biophobic animal species in three habitats. On a zoo tour, respondents want to see species that are large, attractive, strong, and uncommon, but prefer to work professionally with species that are friendly and safe. Students viewed the zoo as a somewhat active, large place, with overall positive connotations. However, it ranks lower than the wild animal park and the nature reserve on the value dimension. Species are considered less active and less strong when caged than when free in their natural habitat or in an animal sanctuary. The different habitats had less effect in the value dimension. This is true for both charismatic and biophobic species.     

A Regression-Based Differential Expression Detection Algorithm for Microarray Studies with Ultra-Low Sample Size

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED). Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.     

Profiling Expression Patterns and Isolating Differentially Expressed Genes by cDNA Microarray System with Colorimetry Detection

A high-density cDNA microarray with colorimetry detection system to simultaneously monitor the expression of many genes on nylon membrane is described and characterized. To quantify the expression of genes and to isolate differentially expressed genes, the southern hybridization process on filter membranes was employed. The levels of gene expression were represented by color intensities generated by colorimetric reactions in place of hazardous radioisotopes or costly laser-induced fluorescence detection. The gene expression patterns on nylon membranes were digitized by devices such as an economical flatbed scanner or a digital camera. The quantitative information of gene expression was retrieved by image analysis software. Quantitative comparison of the northern dot-blotting method with the microarray system is described. Applications employing single-color detection as well as dual-color detection to isolate differentially expressed genes among thousands of genes are demonstrated.     

Integrated Capture and Spectroscopic Detection of Viruses

The goal of this work is to develop an online monitoring scheme for detection of viruses in flowing drinking water. The approach applies an electrodeposition process that is similar to the use of charged membrane filters previously employed for collection of viruses from aqueous samples. In the present approach, charged materials are driven onto a robust optical sensing element which has high transparency to infrared light. A spectroscopic measurement is performed using the evanescent wave that penetrates no more than 1 μm from the surface of an infrared optical element in an attenuated total reflectance measurement scheme. The infrared measurement provides quantitative information on the amount and identity of material deposited from the water. Initial studies of this sensing scheme used proteins reversibly electrodeposited onto germanium chips. The results of those studies were applied to design a method for collection of viruses onto an attenuated total reflectance crystal. Spectral signatures can be discriminated between three types of protein and two viruses. There is the potential to remove deposited material by reversing the voltage polarity. This work demonstrates a novel and practical scheme for detection of viruses in water systems with potential application to near-continual, automated monitoring of municipal drinking water.Despite the application of multibarrier, conventional treatment approaches for municipal water, disease outbreaks associated with tap water continue to occur in the United States (37). An etiological agent is not determined in approximately half of all identified drinking water outbreaks; however, the characteristic symptomatology of the causative agent frequently indicates a viral pathogen. The need for rapid and effective methods of virus collection and detection is apparent for the assurance of water security and water quality and certainly also for medical diagnostics.Commercial systems exist for continual monitoring of municipal drinking water for parameters such as pH, total organic carbon, turbidity, and salt (electrical conductivity). Biological monitoring schemes are available to quantify bacteria, spores, and parasites based on their size or their light scattering or absorbing properties (2, 3, 9). No such approach is available for viruses, which have a smaller size and present a sizeable health concern. Conventional virus detection methods are performed in an off-line manner. These methods have high specificity but are costly, time-consuming, require significant laboratory preparation, and have difficulties adapting to new emerging viruses.Development of the best available technology for effective monitoring of viral pathogens is critical for evaluating and maintaining potable water sources, treatment reliability, and posttreatment distribution water quality. Current methods of virus detection in environmental samples are compromised by the presence of inhibitory compounds, such as humic and fulvic acids, and detection of nonviable microbes (PCR) or by toxicity and lengthy assay times (conventional cell culture), conditions often leading to false-positive or false-negative results (23). Although the use of an integrated cell culture/PCR method has been shown to overcome major flaws of each individual method (1, 22, 24), this approach is neither automated nor rapid.Sampling from water systems (source waters and treated water) for detection of viral pathogens is usually performed with either positively charged membranes, which allow fluid to pass through the filter and collect viruses based on charge, or hollow fiber concentrators, which allow fluid to move across the membrane surface rather than being forced through and concentrate viruses by removal of liquid and larger molecules. In neutral solutions and most environmental drinking water sources, viruses are negatively charged. Adsorption to hollow fiber or filter surfaces is largely due to electrostatic and hydrophobic interactions and is controlled by environmental factors, such as pH and electrolytes (16). Once adsorbed to electrocharged filters, viruses are typically eluted via high-pH buffers or bioflocculants, such as beef extract. Collected materials are then analyzed using culture or primer-specific molecular detection methods. We aim to replace one of these fibers within a hollow fiber concentrator with an optically addressable fiber for spectroscopic detection of viruses deposited using electrophoretic collection, similar in process to commercial electronic air filters.The long-term goal of the present work is to develop an automatable means to detect viruses in aqueous samples using electrodeposition to capture viruses on the surfaces of optical fibers for infrared spectroscopic characterization and identification. Infrared spectroscopy is noninvasive and can provide information in minutes on the composition of a material. The components of a virus (nucleic acids, proteins, phospholipids, and other small molecules) present distinct vibrational fingerprints in the infrared (10-12) which can be used to identify and quantify the type of virus. Other materials present in typical drinking water systems produce minimal signals.Since infrared light is low energy (compared to UV or visible light), the sample may be repeatedly probed without causing damage, permitting continual measurement over the deposition process (10, 13). The vibrational spectrum collected provides an infrared signature very specific to each chemical or biological species. Spectra are typically collected over the range of 4,000 to 620 cm⁻¹ (2.50 to 16.13 μm), which contains the fundamental vibrations and overtones of many biochemicals, including proteins, nucleic acids, phosphates, ammonia, and lipids. For ease of interpretation, the spectral regions are divided into three zones (29). The first, 3,000 to 2,800 cm⁻¹, contains two primary bands at 2,852 cm⁻¹ and 2,922 cm⁻¹, which are attributed to CH₂ asymmetric and symmetric vibrations, respectively. CH₂-containing compounds are present predominantly in long-chain hydrocarbons, such as lipids. The two lower-intensity bands at 2,874 cm⁻¹ and 2,960 cm⁻¹ correspond to the symmetric and asymmetric CH₃ vibrations, respectively, found in lipids and proteins (25). The second (1,700 to 1,400 cm⁻¹) region contains the amide I (1,690 to 1,630 cm⁻¹) and amide II (1,548 cm⁻¹) features typical of proteins. The third spectral region, between 1,100 and 900 cm⁻¹, contains primarily C—O—C and C—O ring vibrations due to carbohydrates and P=O and P—O—P, representative of nucleic acids and phospholipids (18).The reason for the use of Fourier transform infrared (FTIR) spectroscopy in remote optical sensing is the recent availability of infrared transmitting fibers with low losses and sufficient chemical durability (13, 14). Chalcogenide glasses are one of very few materials that combine large optical windows in the infrared, low optical losses, chemical durability, and the ability to be drawn into fibers (15, 35). These glasses also have semiconducting properties similar to those of silicon and therefore have the appropriate electrical properties for use as an electrode during electrophoretic collection of negatively charged viruses. In the present work, we demonstrate the proof of concept for an electrophoretic optical sensor using a germanium (Ge) attenuated total reflectance (ATR) crystal with transparency from 2 to 13 μm in wavelength that spans the region of interest for identification of viral species. Ge is also a good semiconductor and can therefore act as both an optical element and an electrode. Charge-based collection and deposition of viruses have been demonstrated for a number of applications, including collection of viruses on sand and FeO particles and in column chromatography (19, 21, 31, 33). To our knowledge, this approach has not been previously applied by combining electrodeposition with infrared analysis.