The “Window <Emphasis Type="Italic">t</Emphasis> test”: a simple and powerful approach to detect differentially expressed genes in microarray datasets

This work focuses on differential expression analysis of microarray datasets. One way to improve such statistical analyses is to integrate biological information in the design of these analyses. In this paper, we will use the relationship between the level of gene expression and variability. Using this biological information, we propose to integrate the information from multiple genes to get a better estimate of individual gene variance, when a small number of replicates are available, to increase the power of the statistical analysis. We describe a strategy named the “Window t test” that uses multiple genes which share a similar expression level to compute the variance which is then incorporated a classic t test. The performances of this new method are evaluated by comparison with classic and widely-used methods for differential expression analysis (the classic Student t test, the Regularized t test (reg t test), SAM, Limma, LPE and Shrinkage t). In each case tested, the results obtained were at least equivalent to the best performing method and, in most cases, outperformed it. Moreover, the Window t test relies on a very simple procedure requiring small computing power compared with other methods designed for microarray differential expression analysis. Electronic Supplementary Material  Supplementary material is available for this article at and is accessible for authorized users.     

Indoor airborne fungi as risk factors in IgE-mediated respiratory allergy

The purpose of this epidemiological study was to assess respiratory allergy in relation to the presence of indoor airborne fungi. The relationship between IgE-mediated respiratory allergy (skin test positivity) and the presence of fungi (CFU/m³) in the indoor environments of 104 subjects was assessed in a cross-sectional study by controlling for extraneous variables (age, gender, predisposition, asthma, rhinitis, skin positivity to ragweed and mite, and smoking). The qualitative and quantitative measurements of airborne seasonal fungi (Alternaria spp. andCladosporium spp.) and non-seasonal airborne fungi (Penicillium spp. andAspergillus spp.) were taken in the subjects’ indoor environments twice in a 2-year period by volumetric methods (Burkard Personal Sampler). There was a significant association between skin test positivity to seasonal fungi and to ragweed (Adj. OR=3.42, CI=1.76–6.66). There was no association between skin test positivity to seasonal fungi and asthma (Adj. OR=0.52, CI=0.28–0.98), but a significant association was found between skin test positivity to seasonal fungi and rhinitis (Adj. OR=5, CI=2.03–12.32). In a logistic regression analysis (maximum likelihood estimates—model A), no statistical association was found indoors between skin prick test positivity to seasonal fungi (Alternaria and/orCladosporium) and airborneAlternaria and/orCladosporium concentrations (Adj. OR=1.18, CI=0.66–2.07). There was a significant association between skin prick test positivity to seasonal fungi and to non-seasonal fungi (Adj. OR=12.81, CI=1.67–98.34). There was no association between asthma and airbornePenicillium concentrations (Adj. OR=1.86, CI=0.47–7.33) nor between rhinitis and airbornePenicillium concentrations (Adj. OR=0.18, CI=0.03–1.19). In another logistic regression analysis (maximum likelihood estimates — model B) using non-seasonal fungi (Aspergillus andPenicillium), no statistical association was found indoors between skin prick test positivity to non-seasonal fungi and airbornePenicillium concentrations (Adj. OR=0.33, CI=0.07–1.69). These findings suggest an association between rhinitis and seasonal fungi. In the rhinitis stratum, subjects who had skin test positivity to ragweed had a higher risk of being sensitive to seasonal airborne fungal allergens. Subjects with non-seasonal fungal allergy had a high relative risk if they were also allergic to seasonal fungi. There was no association between asthma and airborne fungi, as the epidemiological study (cross-sectional design), by definition, does not allow an etiological evaluation of chronic disease. This would require a longitudinal study, i.e. the measurement of repeated exposure as an independent variable (allergen) and repeated measurement as a function of the disease as outcome in humans as a dependent variable.     

Evaluation of an enzyme-linked immunosorbent assay (ELISA) for the detection ofCampylobacter jejuni antibodies,and comparison with a complement fixation test (CFT)

An enzyme-linked immunosorbent assay (ELISA) was developed for the detection of total anti-Campylobacter immunoglobulins in human sera. In this assay disintegratedCampylobacter bacteria were used as the antigen. Absorption tests including other possibly enteropathogenic bacterial species showed that the ELISA system displayed a high immunological specificity forCampylobacter. Using this ELISA it was found that in about 80% ofCampylobacter patients theseCampylobacter antibodies are produced to almost maximal levels within 8 days after onset of disease, and that they may persist for at least 4 months. Indeed,Campylobacter antibodies were demonstrated at low levels in a large number of control sera. However, accepting an antibody titre of 1: 640 as indicative ofCampylobacter infection, the statistical sensitivity of the ELISA system was 77% and the specificity 95%. In an epidemiological survey a high association was demonstrated between the severity ofCampylobacter-related symptoms and antibody titre values. Assessment ofCampylobacter antibody titres by means of this ELISA and by a complement fixation test in 92 sera from index patients and contacts with and without symptoms showed a high association of results.     

A copper-transporting ATPase BcCCC2 is necessary for pathogenicity of Botrytis cinerea

Copper is an essential trace element that serves as a cofactor for numerous enzymes. In eukaryotes, copper-transporting ATPases deliver copper to various copper-containing proteins in the trans-golgi network. This study identified a copper-transporting ATPase gene BcCcc2 in a fungus pathogenic to plants, Botrytis cinerea. We investigated the biological roles of BcCCC2 by generating null mutants for BcCcc2. Melanization, conidiation and the formation of sclerotia were severely affected in ∆BcCcc2 mutants. Moreover, a pathogenicity assay using tomato leaves and carnation petals revealed the mutants to be nonpathogenic. Further analysis indicated that they formed fewer appressoria and infection cushions than the wild-type. These structures were aberrant in morphology and in many cases had a significantly reduced ability to penetrate the plant epidermis. An assay also indicated that ∆BcCcc2 mutants were defective in infection through wounds. BcCCC2 is necessary not only for penetrating a host but also for fungal growth within plant tissues. Our results also imply that B. cinerea requires copper-containing proteins for infection that are inactive in the absence of the copper-transporting ATPase BcCCC2.     

Generation of white mold disease-resistant sunflower plants expressing human lysozyme gene

Sunflower plants were transformed via co-cultivation of previously bombarded hypocotyl explants with Agrobacterium tumefaciens harboring the plasmid pNGL that contains the human lysozyme gene. The transformed shoots were selected using kanamycin and regenerated plants were analyzed using histochemical β-glucuronidase assay. Southern, Western and Northern blot analyses indicated the transfer, expression and stable integration of the foreign DNA into the sunflower genome. Resistance against the phytopathogenic fungus Sclerotinia sclerotiorum, which causes white mold disease, was confirmed using a phytopathogenic test and microscopic observation of the infection process.     

Forecasting infections of the red rot disease on Porphyra yezoensis Ueda (Rhodophyta) cultivation farms

Pythium porphyrae is a fungal pathogen responsible for red rot disease of the seaweed Porphyra (Rhodophyta). Infection forecasts of Porphyra by P. porphyrae were estimated from the epidemiological observations of Porphyra thalli and numbers of zoospore of P. porphyrae in laboratory and cultivation areas. Four features of forecasting infections were determined by relating zoospore concentrations to the incidence of thallus infection; infection (in more than 1000 zoospores L⁻¹), microscopic infection [less than 2 mm in diameter of lesion (in from 2000 to 3000 zoospores L⁻¹)], macroscopic infection [more than 2 mm in diameter of lesion (in from 3000 to 4000 zoospores L⁻¹), and thallus disintegration (in more than 4000 zoospores L⁻¹). High zoospore concentrations led to more infection. The tendency that zoospore concentration of P. porphyrae increased with the rate of infection of Porphyra thalli was generally observed in forecasting infections in both the laboratory and in cultivation areas. Based on the Porphyra cultivation areas, the accuracy and consistency of forecasting infections suggest that this method could be employed to manage and control red rot disease.     

Strategies for data analyses in a high resolution 1H NMR based metabolomics study of a mouse model of Batten disease

Using an NMR based approach, employing both solution state and high resolution magic angle spinning (HR MAS) ¹H NMR spectroscopy, in conjunction with an array of statistical methods, we report cerebral metabolic deficits in a mouse model of Batten disease (Cln3 null mutant mice). Batten disease is the most common progressive neurodegenerative disorder of childhood and is caused by mutations in the Cln3 gene. In particular, brain tissue from Cln3 mice was characterised by increased concentrations of glutamine, myo-inositol, scyllo-inositol, aspartate and lactate, alongside decreased concentrations of N-acetyl-l-aspartate (NAA), N-acetyl-l-glutamate (NAG), γ-amino butyric acid (GABA), glutamate and creatine. Accompanying changes in lipid deposition were also detected in intact cortical tissue by HR MAS ¹H NMR spectroscopy. To realise the true potential of metabolomic datasets necessitates a comprehensive analysis of the data, such that useful biological information can be extracted and used to generate hypotheses which can be further tested and refined. We found that using a combination of univariate and multivariate analyses, a maximal number of metabolic deficits were successfully identified. In particular the complementary nature of the statistical approaches allowed the definition of changes which were relative, absolute or simply a change in variance, allowing a greater understanding of the disease processes detected.     

Delayed-type Hypersensitivity Response to Crude and Fractionated Antigens from Fonsecaea pedrosoi CMMI 1 Grown in Different Culture Media

Chromoblastomycosis is a subcutaneous fungal disease caused by dematiaceous fungi, especially by Fonsecaea pedrosoi, regarded as its major causative agent in Brazil. In recent years there has been a decline in the use of skin testing for delayed-type hypersensitivity (DTH) in epidemiological surveys of fungal infections, mainly because of the unpredictability of positive reactions and lack of specificity of the antigens used. The aim of the present study was to assess delayed-type skin tests in guinea pigs experimentally infected with F. pedrosoi using exoantigens prepared from two culture filtrates. Sixteen adult male guinea pigs were inoculated intratesticularly with fungal cells and submitted to sensitivity assays 4 weeks after inoculation. They received an intradermal injection with crude and fractionated antigens from Alviano’s and Smith’s cultures, and were assessed 24 and 48 h thereafter. Except for one animal, all of them had positive indurations after 48 h. There were no statistical differences between the measurements at 24 and 48 h for each exoantigen used, neither among the induration measurements at 48 h when different preparations were compared. Our results suggest that a delayed-type skin test using antigens produced in synthetic media may be useful for the assessment of primary exposure to chromoblastomycosis.     

桑椹肥大性菌核病病原菌生物学特性及流行性

【目的】对桑椹灾害性真菌病害——桑椹肥大性菌核病病原菌,即桑实杯盘菌(Ciboria shiraiana)的生物学特性进行研究,分析其流行性。【方法】采用人工接种、调查等研究方法,对C.shiraiana在无性生长阶段中菌丝侵染能力,菌核的休眠期,有性生长阶段中子囊孢子的结构、释放、数目以及萌发等进行研究,并对菌核萌发的物候期进行调查。【结果】C.shiraiana菌丝对桑雌花没有侵染能力;C.shiraiana菌核具有休眠期,低温处理6周以上的菌核才能萌发形成子囊盘;1个菌核可萌发1–15个子囊盘,直径为1.5 cm的子囊盘能产生高达(5.6–6.3)×10~7个子囊孢子;C.shiraiana子囊孢子在酸性环境中的萌发率明显高于在中性和碱性环境中的萌发率;C.shiraiana菌核萌发形成子囊盘产生子囊孢子的物候期,从1月下旬开始到4月中旬结束,其中在3月中旬萌发子囊盘的数目达到最高值。【结论】桑椹肥大性菌核病属于典型的流行性侵染病,在果桑栽培上容易造成毁灭性危害,生产上必须高度重视该病的防控。     

Wild type and <Emphasis Type="Italic">H43Y</Emphasis> variant of human <Emphasis Type="Italic">TRIM5α</Emphasis> show similar anti-human immunodeficiency virus type 1 activity both in vivo and in vitro

Polymorphisms in human genes have been shown to affect the rate of disease progression to acquired immune deficiency syndrome in human immunodeficiency virus type 1 (HIV-1)-infected individuals. Recently, tripartite motif 5α (TRIM5α) was identified as a factor that confers resistance to HIV-1 infection in Old World monkey cells. Subsequently, Sawyer et al. (Curr Biol 16:95–100, 2006) reported a single nucleotide polymorphism (H43Y) in the human TRIM5α gene and TRIM5α protein with 43Y was found to lose its ability to restrict HIV-1. In the present study, we reevaluated effects of this allele on in vitro anti-HIV-1 activity as well as on HIV-1 disease progression in European and Asian cohorts of HIV-1-infected individuals. Our epidemiological and molecular biological findings clearly indicate H43Y has a very minor effect on anti-HIV-1 activity of TRIM5α, suggesting that this allele is immaterial, at least in HIV-1-infected Europeans and Asians.     

Beyond immunity: quantifying the effects of host anti-parasite behavior on parasite transmission

A host’s first line of defense in response to the threat of parasitic infection is behavior, yet the efficacy of anti-parasite behaviors in reducing infection are rarely quantified relative to immunological defense mechanisms. Larval amphibians developing in aquatic habitats are at risk of infection from a diverse assemblage of pathogens, some of which cause substantial morbidity and mortality, suggesting that behavioral avoidance and resistance could be significant defensive strategies. To quantify the importance of anti-parasite behaviors in reducing infection, we exposed larval Pacific chorus frogs (Pseudacris regilla) to pathogenic trematodes (Ribeiroia and Echinostoma) in one of two experimental conditions: behaviorally active (unmanipulated) or behaviorally impaired (anesthetized). By quantifying both the number of successful and unsuccessful parasites, we show that host behavior reduces infection prevalence and intensity for both parasites. Anesthetized hosts were 20–39% more likely to become infected and, when infected, supported 2.8-fold more parasitic cysts. Echinostoma had a 60% lower infection success relative to the more deadly Ribeiroia and was also more vulnerable to behaviorally mediated reductions in transmission. For Ribeiroia, increases in host mass enhanced infection success, consistent with epidemiological theory, but this relationship was eroded among active hosts. Our results underscore the importance of host behavior in mitigating disease risk and suggest that, in some systems, anti-parasite behaviors can be as or more effective than immune-mediated defenses in reducing infection. Considering the severe pathologies induced by these and other pathogens of amphibians, we emphasize the value of a broader understanding of anti-parasite behaviors and how co-occurring stressors affect them.     

Genetic Polymorphism Characteristics of Brucella canis Isolated in China

In China, brucellosis is an endemic disease typically caused by Brucella melitensis infection (biovars 1 and 3). Brucella canis infection in dogs has not traditionally recognized as a major problem. In recent years however, brucellosis resulting from Brucella canis infection has also been reported, suggesting that infections from this species may be increasing. Data concerning the epidemiology of brucellosis resulting from Brucella canis infection is limited. Therefore, the purpose of this study was to assess the diversity among Chinese Brucella canis strains for epidemiological purposes. First, we employed a 16-marker VNTR assay (Brucella MLVA-16) to assess the diversity and epidemiological relationship of 29 Brucella canis isolates from diverse locations throughout China with 38 isolates from other countries. MLVA-16 analysis separated the 67 Brucella canis isolates into 57 genotypes that grouped into five clusters with genetic similarity coefficients ranging from 67.73 to 100%. Moreover, this analysis revealed a new genotype (2-3-9-11-3-1-5-1:118), which was present in two isolates recovered from Guangxi in 1986 and 1987. Second, multiplex PCR and sequencing analysis were used to determine whether the 29 Chinese Brucella canis isolates had the characteristic BMEI1435 gene deletion. Only two isolates had this deletion. Third, amplification of the omp25 gene revealed that 26 isolates from China had a T545C mutation. Collectively, this study reveals that considerable diversity exists among Brucella canis isolates in China and provides resources for studying the genetic variation and microevolution of Brucella.     

Ring test assessment of the mKir2.1 growth based assay in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> using parametric models and model-free fits

Inward rectifying K⁺ (Kir) channels are a subfamily of the potassium channel superfamily. They mediate potassium influx into the cells, a process responding to the polarization state, a variety of intracellular messengers and specific auxiliary proteins, thereby they are involved in important physiological processes such as the pacemaker activity in the heart, insulin release, and potassium uptake in glial cells. The Saccharomyces cerevisiae mKir2.1 in vitro assay was subjected to a ring test assessment. Compound-associated mKir2.1 modulating effects were detected by growth determination of functionally complemented S. cerevisiae cells in a 96-well format within 15 h. Dose–response diagrams and EC₅₀ value calculations were determined by parametric model and model-free fits using cubic spline interpolation. These characteristics were evaluated by statistical methods to determine reproducibility among working groups. Nonparametric bootstrap simulations of the variability of the data revealed that EC₅₀ values of the mKir2.1 indicator strain were well-matched (81–92 μM), enabling unambiguous quantitative statements about inhibitory effects and no significant influence of the different laboratory conditions. Limitations of the assay include compounds/samples that are either insoluble under the conditions of the test or strongly cytotoxic to yeast. Thus, the described test is a sensitive and reliable tool that can be used in different laboratories and is applicable in drug discovery and development as simple and reliable prescreening procedure.     

The telomere lengthening conundrum – it could be biology

Longitudinal studies of human leucocyte telomere length often report a percentage of individuals whose telomeres appear to lengthen. However, based on theoretical considerations and empirical data, Steenstrup et al. (Nucleic Acids Research, 2013, vol 41(13): e131) concluded that this lengthening is unlikely to be a real biological phenomenon and is more likely to be an artefact of measurement error. We dispute the logic underlying this claim. We argue that Steenstrup et al.'s analysis is incomplete because it failed to compare predictions derived from assuming a scenario with no true telomere lengthening with alternative scenarios in which true lengthening occurs. To address this deficit, we built a computational model of telomere dynamics that allowed us to compare the predicted percentage of observed telomere length gainers given differing assumptions about measurement error and the true underling dynamics. We modelled a set of scenarios, all assuming measurement error, but both with and without true telomere lengthening. We found a range of scenarios assuming some true telomere lengthening that yielded either similar or better quantitative fits to the empirical data on the percentage of individuals showing apparent telomere lengthening. We conclude that although measurement error contributes to the prevalence of apparent telomere lengthening, Steenstrup et al.'s conclusion was too strong, and current data do not allow us to reject the hypothesis that true telomere lengthening is a real biological phenomenon in epidemiological studies. Our analyses highlight the need for process‐level models in the analysis of telomere dynamics.     

Detecting Natural Selection at the Molecular Level: A Reexamination of Some “Classic” Examples of Adaptive Evolution

An important criterion used to detect adaptive evolution in DNA sequence data is ω_i > 1, where ω_i is the ratio of nonsynonymous to synonymous substitution rates in lineage i. However, the evaluation of multiple ω_i within a phylogenetic tree can easily inflate the statistical type I error rate. We developed two rigorous methods of analysis that avoid this and other potential pitfalls. We applied these methods to four published examples of adaptive evolution. One case was strongly supported by our reanalysis (abalone sperm lysin), and one was weakly supported (baboon α-globin), but two examples (primate lysozyme and Antarctic fish β-globin) did not show significant evidence of adaptive evolution. Our first method is a “bottom-up” hierarchical maximum likelihood approach, which (1) tests for significant heterogeneity in ω across the phylogeny, (2) locates its source using a sequence of planned comparisons, and (3) tests homogeneous groups of ω for ω > 1, using a modified level of significance that incorporates the pretesting. The second method is a “top-down” log-linear analysis based on estimates of nonsynonymous and synonymous substitutions in pairs of lineages. The log-linear test is applied to pairs of lineages joined at progressively deeper nodes. For each pair, the analysis simultaneously tests for adaptive evolution (ω > 1), a shift in natural selection (ω₁ ≠ω₂), and unequal evolution rate (the relative rate test). In both tests, we emphasized that the criterion ω₁ ≠ ω₂ is an important additional indicator of a phylogenetic shift in the balance between natural selection and genetic drift between two related lineages. [Reviewing Editor: Dr. John Huelsenbeck]     

Lyme borreliosis—analysis of the trends in Slovakia, 1999–2008

Lyme borreliosis (LB) presents as one of the most frequent tick-borne diseases in Europe with more than 85,000 reported cases every year. The transport of this disease on humans is by tick species of the genus Ixodes. In our work, we aimed to perform a retrospective analysis of the incidence and seasonality of Lyme borreliosis during the period 1999–2008 in Slovakia. For our analysis, we used all the relevant data about the patients with Lyme borreliosis reported in the Epidemiological Informative System of Communicable Diseases in Slovakia during the decade of 1999–2008. During the observed period, there were 7,349 reported cases of LB in Slovakia. Whereas the incidence of early localized infection did not change during the observed period, there was a significant increase in the incidence of early disseminated infection and late persistent infection of LB. Seventy per cent of all patients was infected by tick bite. LB was more frequently reported in females than in males (56.1% vs. 43.9%; p < 0.05), and the most involved age group was the productive age (15–64 years). The incidence of disseminated infection and persistent infection was rising with increasing age. Regarding the seasonality of LB, we found the highest incidence during the summer months. Comparing the situation of LB in 1999 and 2008, significant increase in the number of reported cases was in April and June and from September to November (p < 0.05). Our epidemiological analysis confirmed that Lyme borreliosis requires increased attention due to its increasing incidence.     

毒力基因yqeH功能分析及对禽致病性大肠杆菌致病性的影响

【背景】禽致病性大肠杆菌(avian pathogenic Escherichia coli,APEC)可引起禽类急性或亚急性感染,在近年新发现的大肠杆菌Ⅲ型分泌系统2 (Escherichia coli type III secretion system 2,ETT2)中,毒力基因yqeH对其致病性的影响尚不明确。【目的】探究yqeH在APEC致病过程中的作用,为后期深入研究ETT2致病机制奠定基础。【方法】利用Red同源重组技术构建yqeH缺失株ΔyqeH及其回复株CΔyqeH,通过运动性、生物被膜形成能力、抗逆性、抗血清杀菌能力等试验分析yqeH对APEC生物学功能的影响,并通过细胞黏附、侵袭试验、致病力测定及荧光定量PCR检测细胞炎性因子转录水平,探究yqeH对APEC感染宿主的影响。【结果】构建了缺失株ΔyqeH和回复株CΔyqeH;生物学特性试验结果表明,与野生株APEC81相比,缺失株ΔyqeH生物被膜形成能力、运动能力降低,对酸、碱、渗透压、氧化休克的耐受力降低,抗血清杀菌能力及致病力显著降低;与野生株APEC81相比,缺失株ΔyqeH对鸡气管黏膜上皮细胞的黏附及侵袭能...     

Words in DNA sequences: some case studies based on their frequency statistics

 One of the critical requirements of data analysis involving large DNA sequences is an effective statistical summarization of those sequences. In this article DNA sequences have been analyzed based on word frequencies. Our analysis focuses on the detection of structural signature of a genome reflected in word frequencies and identification of phylogenetic relationships among different species reflected in the variation of word distributions in their DNA sequences. We have carried out a statistical study of the complete genome of baker's yeast, of various ribosomal RNA sequences from different prokaryotic and eukaryotic organisms and of the full genomes of some bacteriophages. Our exploratory analysis amply demonstrates the usefulness of DNA word frequencies in reducing the dimensionality of large sequences while retaining some of the structural information there that can have biological significance. Some conceptual issues that arise in course of our investigation have been addressed. A few interesting problems related to the statistics of DNA words have been pointed out with some indication of their possible solutions. The work has been partially motivated by the fact that sequence alignment and homology techniques that are quite popular for comparing and analyzing relatively smaller DNA sequences of nearly equal sizes are not applicable to data consisting of large sequences with widely varying sizes, which may contain segments with unknown or no biological functions, and consequently their comparison through functional homology is either impossible or extremely difficult. Received: 15 October 2000 / Revised version: 8 October 2002 Published online: 28 February 2003 Current address: CF186, Salt lake, Calcutta 700064, India Research presented here was supported in part by a grant from Indian Statistical Institute. Key words or phrases: Average linkage clustering – Chernoff's faces – Dendrograms – DNA words – F-ranks of words – F-ratios of words – l ₁-distance – Phylogenetic relationships – Rank correlation – Single linkage clustering