Revealing the Hidden Relationship by Sparse Modules in Complex Networks with a Large-Scale Analysis

One of the remarkable features of networks is module that can provide useful insights into not only network organizations but also functional behaviors between their components. Comprehensive efforts have been devoted to investigating cohesive modules in the past decade. However, it is still not clear whether there are important structural characteristics of the nodes that do not belong to any cohesive module. In order to answer this question, we performed a large-scale analysis on 25 complex networks with different types and scales using our recently developed BTS (bintree seeking) algorithm, which is able to detect both cohesive and sparse modules in the network. Our results reveal that the sparse modules composed by the cohesively isolated nodes widely co-exist with the cohesive modules. Detailed analysis shows that both types of modules provide better characterization for the division of a network into functional units than merely cohesive modules, because the sparse modules possibly re-organize the nodes in the so-called cohesive modules, which lack obvious modular significance, into meaningful groups. Compared with cohesive modules, the sizes of sparse ones are generally smaller. Sparse modules are also found to have preferences in social and biological networks than others.     

IP-10 Can Be Measured in Dried Plasma Spots in Patients with Chronic Hepatitis C Infection

The chemokine IP-10 (CXCL10) is a candidate marker for hepatitis C virus (HCV) fibrosis monitoring. The aim of this proof-of-concept study is to assess if IP-10 measurements from dried plasma spots (DPS) are accurate in HCV-infected patients with either minimal or significant fibrosis. We measured IP-10 levels in plasma and DPS of 21 HCV-infected patients with cirrhosis and 19 patients with no/little fibrosis (determined with FibroScan). Cirrhotic patients had significantly higher levels of IP-10 compared to patients with minimal fibrosis. DPS and plasma measurements of IP-10 are comparable and the correlation was excellent (r² = 0.97, p<0.0001). The DPS based method for IP-10 detection performs well in HCV-infected patients with either minimal or significant fibrosis.     

Alterations in SiRNA and MiRNA Expression Profiles Detected by Deep Sequencing of Transgenic Rice with SiRNA-Mediated Viral Resistance

RNA-mediated gene silencing has been demonstrated to serve as a defensive mechanism against viral pathogens by plants. It is known that specifically expressed endogenous siRNAs and miRNAs are involved in the self-defense process during viral infection. However, research has been rarely devoted to the endogenous siRNA and miRNA expression changes under viral infection if the resistance has already been genetically engineered in plants. Aiming to gain a deeper understanding of the RNA-mediated gene silencing defense process in plants, the expression profiles of siRNAs and miRNAs before and after viral infection in both wild type and transgenic anti-Rice stripe virus (RSV) rice plants were examined by small RNA high-throughput sequencing. Our research confirms that the newly generated siRNAs, which are derived from the engineered inverted repeat construct, is the major contributor of the viral resistance in rice. Further analysis suggests the accuracy of siRNA biogenesis might be affected when siRNAs machinery is excessively used in the transgenic plants. In addition, the expression levels of many known miRNAs are dramatically changed due to RSV infection on both wild type and transgenic rice plants, indicating potential function of those miRNAs involved in plant-virus interacting process.     

Disease Interactions in a Shared Host Plant: Effects of Pre-Existing Viral Infection on Cucurbit Plant Defense Responses and Resistance to Bacterial Wilt Disease

Both biotic and abiotic stressors can elicit broad-spectrum plant resistance against subsequent pathogen challenges. However, we currently have little understanding of how such effects influence broader aspects of disease ecology and epidemiology in natural environments where plants interact with multiple antagonists simultaneously. In previous work, we have shown that healthy wild gourd plants (Cucurbita pepo ssp. texana) contract a fatal bacterial wilt infection (caused by Erwinia tracheiphila) at significantly higher rates than plants infected with Zucchini yellow mosaic virus (ZYMV). We recently reported evidence that this pattern is explained, at least in part, by reduced visitation of ZYMV-infected plants by the cucumber beetle vectors of E. tracheiphila. Here we examine whether ZYMV-infection may also directly elicit plant resistance to subsequent E. tracheiphila infection. In laboratory studies, we assayed the induction of key phytohormones (SA and JA) in single and mixed infections of these pathogens, as well as in response to the feeding of A. vittatum cucumber beetles on healthy and infected plants. We also tracked the incidence and progression of wilt disease symptoms in plants with prior ZYMV infections. Our results indicate that ZYMV-infection slightly delays the progression of wilt symptoms, but does not significantly reduce E. tracheiphila infection success. This observation supports the hypothesis that reduced rates of wilt disease in ZYMV-infected plants reflect reduced visitation by beetle vectors. We also documented consistently strong SA responses to ZYMV infection, but limited responses to E. tracheiphila in the absence of ZYMV, suggesting that the latter pathogen may effectively evade or suppress plant defenses, although we observed no evidence of antagonistic cross-talk between SA and JA signaling pathways. We did, however, document effects of E. tracheiphila on induced responses to herbivory that may influence host-plant quality for (and hence pathogen acquisition by) cucumber beetles.     

Mycobacterium marinum Causes a Latent Infection that Can Be Reactivated by Gamma Irradiation in Adult Zebrafish

The mechanisms leading to latency and reactivation of human tuberculosis are still unclear, mainly due to the lack of standardized animal models for latent mycobacterial infection. In this longitudinal study of the progression of a mycobacterial disease in adult zebrafish, we show that an experimental intraperitoneal infection with a low dose (∼35 bacteria) of Mycobacterium marinum, results in the development of a latent disease in most individuals. The infection is characterized by limited mortality (25%), stable bacterial loads 4 weeks following infection and constant numbers of highly organized granulomas in few target organs. The majority of bacteria are dormant during a latent mycobacterial infection in zebrafish, and can be activated by resuscitation promoting factor ex vivo. In 5–10% of tuberculosis cases in humans, the disease is reactivated usually as a consequence of immune suppression. In our model, we are able to show that reactivation can be efficiently induced in infected zebrafish by γ-irradiation that transiently depletes granulo/monocyte and lymphocyte pools, as determined by flow cytometry. This immunosuppression causes reactivation of the dormant mycobacterial population and a rapid outgrowth of bacteria, leading to 88% mortality in four weeks. In this study, the adult zebrafish presents itself as a unique non-mammalian vertebrate model for studying the development of latency, regulation of mycobacterial dormancy, as well as reactivation of latent or subclinical tuberculosis. The possibilities for screening for host and pathogen factors affecting the disease progression, and identifying novel therapeutic agents and vaccine targets make this established model especially attractive.     

Plant Virology and Next Generation Sequencing: Experiences with a Potyvirus

Next generation sequencing is quickly emerging as the go-to tool for plant virologists when sequencing whole virus genomes, and undertaking plant metagenomic studies for new virus discoveries. This study aims to compare the genomic and biological properties of Bean yellow mosaic virus (BYMV) (genus Potyvirus), isolates from Lupinus angustifolius plants with black pod syndrome (BPS), systemic necrosis or non-necrotic symptoms, and from two other plant species. When one Clover yellow vein virus (ClYVV) (genus Potyvirus) and 22 BYMV isolates were sequenced on the Illumina HiSeq2000, one new ClYVV and 23 new BYMV sequences were obtained. When the 23 new BYMV genomes were compared with 17 other BYMV genomes available on Genbank, phylogenetic analysis provided strong support for existence of nine phylogenetic groupings. Biological studies involving seven isolates of BYMV and one of ClYVV gave no symptoms or reactions that could be used to distinguish BYMV isolates from L. angustifolius plants with black pod syndrome from other isolates. Here, we propose that the current system of nomenclature based on biological properties be replaced by numbered groups (I–IX). This is because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable. This study also demonstrated that, where next generation sequencing is used to obtain complete plant virus genomes, consideration needs to be given to issues regarding sample preparation, adequate levels of coverage across a genome and methods of assembly. It also provided important lessons that will be helpful to other plant virologists using next generation sequencing in the future.     

Plant Species Composition Can Be Used as a Proxy to Predict Methane Emissions in Peatland Ecosystems After Land-Use Changes

Land-use change in peatlands affects important drivers of CH₄ emission such as groundwater level and nutrient availability. Due to the high spatial and temporal variability of such environmental drivers, it is hard to make good predictions of CH₄ emissions in the context of land-use changes. Here, we used plant species composition as a stable integrator of environmental drivers of CH₄ emissions. We used weighted averaging regression and calibration to make a direct link between plant species composition and CH₄ flux in an effort to predict values of CH₄ emission for a land-use gradient in two extensive peatland sites. Our predicted CH₄ emissions showed good fit with observed values. Additionally, we showed that a quick characterization of vegetation composition, by the dominant species only, provides equally good predictions of CH₄ emissions. The use of mean groundwater level alone for predicting emissions showed the same predictive power as our models. However, water level showed strong variability in time. Furthermore, the inverse relationship between water level and CH₄ emission can lead to higher errors in predictions at sites with higher CH₄ emission. The performance of our model was comparable with those of mechanistic models developed for natural wetland ecosystems. However, such mechanistic models require complex input parameters that are rarely available. We propose the use of plant species composition as a simple and effective alternative for deriving predictions of CH₄ emissions in peatlands in the context of land-use change.     

Persistent Hz-1 Virus Infection in Insect Cells: Evidence for Insertion of Viral DNA into Host Chromosomes and Viral Infection in a Latent Status

Persistent/latent viral infections of insect cells are a prominent though poorly understood phenomenon. In this study, the long-term association between the Hz-1 virus and insect host cells, conventionally referred to as persistent viral infection, is described. With the aid of a newly developed fluorescent cell-labeling system, we found that productive viral replication occurs by spontaneous viral reactivation in fewer than 0.2% of persistently infected cell lines over a 5-day period. Once viral reactivation takes place, the host cell dies. The persistently infected cells contain various amounts of viral DNA, and, in an extreme case, up to 16% of the total DNA isolated from infected cells could be of viral origin. Both pulsed-field gel electrophoresis and in situ hybridization experiments showed that some of these viral DNA molecules are inserted into the host chromosomes but that the rest of viral DNA copies are free from host chromosomes. Thus, Hz-1 virus is the first nonretroviral insect virus known to insert its genome into the host chromosome during the infection process. These data also suggest that the previously described persistent infection of Hz-1 virus in insect cells should be more accurately referred to as latent viral infection.     

Deep Bisulfite Sequencing of Aberrantly Methylated Loci in a Patient with Multiple Methylation Defects

NLRP7 is a maternal effect gene as maternal mutations in this gene cause recurrent hydatidiform moles, spontaneous abortions and stillbirths, whereas live births are very rare. We have studied a patient with multiple anomalies born to a mother with a heterozygous NLRP7 mutation. By array-based CpG methylation analysis of blood DNA from the patient, his parents and 18 normal controls on Illumina Infinium HumanMethylation27 BeadChips we found that the patient had methylation changes (delta ß ≥ 0.3) at many imprinted loci as well as at 87 CpGs associated with 85 genes of unknown imprinting status. Using a pseudoproband (permutation) approach, we found methylation changes at only 7-24 CpGs (mean 15; standard deviation 4.84) in the controls. Thus, the number of abberantly methylated CpGs in the patient is more than 14 standard deviations higher. In order to identify novel imprinted genes among the 85 conspicuous genes in the patient, we selected 19 (mainly hypomethylated) genes for deep bisulfite amplicon sequencing on the ROCHE/454 Genome Sequencer in the patient and at least two additional controls. These controls had not been included in the array analysis and were heterozygous for a single nucleotide polymorphism at the test locus, so that allele-specific DNA methylation patterns could be determined. Apart from FAM50B, which we proved to be imprinted in blood, we did not observe allele-specific DNA methylation at the other 18 loci. We conclude that the patient does not only have methylation defects at imprinted loci but (at least in blood) also an excess of methylation changes at apparently non-imprinted loci.     

Interactions between Viral and Prokaryotic Pathogens in a Mixed Infection with Cardiovirus and Mycoplasma

In the natural environment, animal and plant viruses often share ecological niches with microorganisms, but the interactions between these pathogens, although potentially having important implications, are poorly investigated. The present report demonstrates, in a model system, profound mutual effects of mycoplasma and cardioviruses in animal cell cultures. In contrast to mycoplasma-free cells, cultures contaminated with Mycoplasma hyorhinis responded to infection with encephalomyocarditis virus (EMCV), a picornavirus, but not with poliovirus (also a picornavirus), with a strong activation of a DNase(s), as evidenced by the TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) immunofluorescence assay and electrophoretic analysis of host DNA. This degradation was reminiscent of that observed upon apoptosis but was caspase independent, judging by the failure of the specific pan-caspase inhibitor Q-VD-OPh to prevent it. The electrophoretic mobility of the enzyme responsible for DNA degradation and dependence of its activity on ionic conditions strongly suggested that it was represented by a DNase(s) of mycoplasma origin. In cells not infected with EMCV, the relevant DNase was dormant. The possibility is discussed that activation of the mycoplasma DNase might be linked to a relatively early increase in permeability of plasma membrane of the infected cells caused by EMCV. This type of unanticipated virus-mycoplasma “cooperation” may exemplify the complexity of pathogen-host interactions under conditions when viruses and microorganisms are infecting the same host. In the course of the present study, it was also demonstrated that pan-caspase inhibitor zVAD(OMe).fmk strongly suppressed cardiovirus polyprotein processing, illustrating an additional pitfall in investigations of viral effects on the apoptotic system of host cells.Traditionally, virologists are predominantly studying properties of individual viruses and much rarely interactions between different viruses. Even less attention is paid to interactions between viruses and microbes, although animal and plant viruses quite often share, in the natural environment, their ecological niches with microorganisms. Interactions of microbes with viruses other than phages are essentially a virgin soil of either virology or microbiology. The scarcity of relevant information may be illustrated by a recent review focused on the interaction between enteric viruses and enteric bacteria (23). There is ground to believe, however, that the impact of microbial flora on viral growth and pathogenicity (and vice versa) is much broader and deeper than is currently thought. One of the reasons for such a belief is the well-known effect of bacteria (and of their metabolic products) on diverse signaling systems of animal cells, in particular those involved in innate immunity (14, 41, 85, 89). A recent relevant example is demonstration that a prokaryotic infection may protect drosophila from a variety of RNA viruses (39). On the other hand, viral infection may significantly alter the outcome of concomitant bacterial infections. For example, it was reported that herpesvirus latency in mice may confer significant resistance to Listeria and Yersinia pathogens (8).The aim of the present report is to demonstrate, in a model system, profound mutual effects of mycoplasma and cardioviruses during their interaction with animal cells. Cardioviruses, a genus in the picornavirus family, are represented by such widely investigated viruses as encephalomyocarditis virus (EMCV) and its strain mengovirus (MV), as well as Theiler''s murine encephalomyelitis virus (TMEV). Cardioviruses are pathogens naturally affecting many animal species, in particular, rodents, pigs, and some primates (49). Recently, TMEV-related viruses have been implicated in human pathology (1, 12, 21, 29, 45, 46, 51, 96). Picornaviruses, which also include such viruses as poliovirus, hepatitis A virus, foot-and-mouth disease virus, and many others, possess a 7.2-8 kb-long single-stranded RNA genome of positive polarity and share general features of their reproduction mechanism (2). The genomic RNA contains a large single reading frame (certain strains of TMEV, but not EMCV, encode also a protein, L*, in an alternative frame; see reference 47) translated into a polyprotein, which is processed into a dozen “mature” proteins by a series of proteolytic events.Interaction of picornaviruses with susceptible cells may have different outcomes: it may result in cytopathic (necrotic) effect (CPE) or apoptotic death, or it may lead to persistent infection. The character of these outcomes has obvious implications for the pathogenesis of the viral disease. Necrotic death is a strong trigger of inflammatory reactions. Apoptosis, which leads to degradation of host DNA and fragmentation of cells into membrane-coated so-called apoptotic bodies and their eventual “consumption” by macrophages and other scavenger cells, could limit not only the spread of the viral progeny but also prevent potential damages to the neighboring cells caused by inflammation. Therefore, apoptosis is generally considered to represent a defensive host reaction. The fate of the picornavirus-infected cell depends on the genetic properties of the both partners of virus-host interaction, as well as on the status of cell differentiation and environmental conditions (3, 13, 69, 70, 79, 80, 86). In particular, cardioviruses may evoke apoptotic reaction in certain, especially partially restrictive, cells (42, 43, 75, 76, 92).Mycoplasmas are the smallest prokaryotic obligate parasites devoid of cell wall and of many synthetic capabilities and able to trigger a variety of diseases, such as pneumonia, uretritis and many others; they also frequently contaminate cultured cells. Mycoplasmas could be attached to plasma membrane of eukaryotic cells but in some cases they are able to invade the cells as well. They may exert a variety of effects on signaling systems of animal cells affecting, in particular, their innate immunity (67, 71).We will demonstrate here that, in several mycoplasma-contaminated cell cultures, infection with EMCV (but not with poliovirus) results in activation of the microorganism-derived DNase(s), which accomplishes degradation of host cell DNA resembling that occurring during apoptosis but which was caspase independent. The same but mycoplasma-free cells respond to EMCV infection with a canonical CPE (70). This type of unanticipated virus-mycoplasma “cooperation” may illustrate the complexity of pathogen-host interactions under conditions when both viruses and microorganisms are present.     

Enterovirus 71 Infection Causes Severe Pulmonary Lesions in Gerbils,Meriones unguiculatus,Which Can Be Prevented by Passive Immunization with Specific Antisera

Neurogenic pulmonary edema caused by severe brainstem encephalitis is the leading cause of death in young children infected by Enterovirus 71 (EV71). However, no pulmonary lesions have been found in EV71-infected transgenic or non-transgenic mouse models. Development of a suitable animal model is important for studying EV71 pathogenesis and assessing effect of therapeutic approaches. We had found neurological disorders in EV71-induced young gerbils previously. Here, we report severe pulmonary lesions characterized with pulmonary congestion and hemorrhage in a gerbil model for EV71 infection. In the EV71-infected gerbils, six 21-day-old or younger gerbils presented with a sudden onset of symptoms and rapid illness progression after inoculation with 1×10^5.5 TCID₅₀ of EV71 via intraperitoneal (IP) or intramuscular (IM) route. Respiratory symptoms were observed along with interstitial pneumonia, pulmonary congestion and extensive lung hemorrhage could be detected in the lung tissues by histopathological examination. EV71 viral titer was found to be peak at late stages of infection. EV71-induced pulmonary lesions, together with severe neurological disorders were also observed in gerbils, accurately mimicking the disease process in EV71-infected patients. Passive transfer with immune sera from EV71 infected adult gerbils with a neutralizing antibody (GMT=89) prevented severe pulmonary lesion formation after lethal EV71 challenge. These results establish this gerbil model as a useful platform for studying the pathogenesis of EV71-induced pulmonary lesions, immunotherapy and antiviral drugs.     

Deceptive color signaling in the night: a nocturnal predator attracts prey with visual lures

The role color signaling plays in the nocturnal condition ofthe terrestrial ecosystem is currently poorly understood. Ingeneral, arthropods active in the night are inconspicuouslycolored. However, in addition to inconspicuously colored dorsum,several genera of nocturnal orb spiders also have conspicuousventrum spots. In this study, we tested whether the inconspicuouslycolored dorsum functioned to reduce spiders‘ visibilityto diurnal predators while the spiders were perching on barkwith ventrum spots well concealed. We also evaluated when spiderssit on webs with conspicuous ventrum spots fully exposed, wouldthey serve as deceptive color signals to lure visually orientatednocturnal prey. We first quantified how diurnal hymenopteranpredators viewed the dorsum and nocturnal lepidopteran preyviewed the ventrum spots of nocturnal orb spiders Neoscona punctigeraby calculating color contrasts. The diurnal color contrast ofspiders’ dorsum when viewed by hymenopteran insects againstbark was lower than the discrimination threshold. However, thenocturnal color contrasts of spiders‘ ventrum spots whenviewed by moths were high. In the field, webs with N. punctigeraintercepted significantly more insects than those without. Whenthe color signal of ventrum spots was altered by paint, webs’prey interception rates decreased significantly. These resultsdemonstrate that even in the nocturnal condition certain terrestrialorganisms exhibit visual lures to attract prey.     

Agrobacterium VirE2 Proteins Can Form a Complex with T Strands in the Plant Cytoplasm

Wild-type VirE2 and VirD2 proteins from Agrobacterium tumefaciens contain nuclear targeting sequences (NLS) that are likely involved in directing transferred T strands to the plant nucleus. An A. tumefaciens virE2 virD2ΔNLS double mutant was able to form tumors on VirE2-producing transgenic tobacco but not on wild-type tobacco. Because this mutant bacterial strain contains no known T-strand nuclear targeting signal, the data indicate that wild-type VirE2 proteins produced by the plant can interact with the T strands in the plant cytoplasm and direct them to the nucleus.     

Sera from Children with Autism Induce Autistic Features Which Can Be Rescued with a CNTF Small Peptide Mimetic in Rats

Autism is a neurodevelopmental disorder characterized clinically by impairments in social interaction and verbal and non-verbal communication skills as well as restricted interests and repetitive behavior. It has been hypothesized that altered brain environment including an imbalance in neurotrophic support during early development contributes to the pathophysiology of autism. Here we report that sera from children with autism which exhibited abnormal levels of various neurotrophic factors induced cell death and oxidative stress in mouse primary cultured cortical neurons. The effects of sera from autistic children were rescued by pre-treatment with a ciliary neurotrophic factor (CNTF) small peptide mimetic, Peptide 6 (P6), which was previously shown to exert its neuroprotective effect by modulating CNTF/JAK/STAT pathway and LIF signaling and by enhancing brain derived neurotrophic factor (BDNF) expression. Similar neurotoxic effects and neuroinflammation were observed in young Wistar rats injected intracerebroventricularly with autism sera within hours after birth. The autism sera injected rats demonstrated developmental delay and deficits in social communication, interaction, and novelty. Both the neurobiological changes and the behavioral autistic phenotype were ameliorated by P6 treatment. These findings implicate the involvement of neurotrophic imbalance during early brain development in the pathophysiology of autism and a proof of principle of P6 as a potential therapeutic strategy for autism.     

Noisy Interlimb Coordination Can Be a Main Cause of Freezing of Gait in Patients with Little to No Parkinsonism

Freezing of gait in patients with Parkinson’s disease is associated with several factors, including interlimb incoordination and impaired gait cycle regulation. Gait analysis in patients with Parkinson’s disease is confounded by parkinsonian symptoms such as rigidity. To understand the mechanisms underlying freezing of gait, we compared gait patterns during straight walking between 9 patients with freezing of gait but little to no parkinsonism (freezing patients) and 11 patients with Parkinson’s disease (non-freezing patients). Wireless sensors were used to detect foot contact and toe-off events, and the step phase of each foot contact was calculated by defining one stride cycle of the other leg as 360°. Phase-resetting analysis was performed, whereby the relation between the step phase of one leg and the subsequent phase change in the following step of the other leg was quantified using regression analysis. A small slope of the regression line indicates a forceful correction (phase reset) at every step of the deviation of step phase from the equilibrium phase, usually at around 180°. The slope of this relation was smaller in freezing patients than in non-freezing patients, but the slope exhibited larger step-to-step variability. This indicates that freezing patients executed a forceful but noisy correction of the deviation of step phase, whereas non-freezing patients made a gradual correction of the deviation. Moreover, freezing patients tended to show more variable step phase and stride time than non-freezing patients. Dynamics of a model of two coupled oscillators interacting through a phase resetting mechanism were examined, and indicated that the deterioration of phase reset by noise provoked variability in step phase and stride time. That is, interlimb coordination can affect regulation of the gait cycle. These results suggest that noisy interlimb coordination, which probably caused forceful corrections of step phase deviation, can be a cause of freezing of gait.