Silencing or permanent activation: host-cell responses in models of persistent Chlamydia pneumoniae infection

Chlamydia pneumoniae causes respiratory infections. In chronic diseases associated with Chlamydia, such as arteriosclerosis, C. pneumoniae is present in a persistent form, which might participate in pathogenesis of chronic inflammatory disease. To elucidate how these intracellular bacteria modulate host-cells during persistence, we compared the expression pattern of a range of host genes after short (24 h) and long (up to 7 days) times of chlamydia infection in HeLa-cells. One day post infection, in three cell-culture models of persistence, namely treatment with penicillin or IFN-gamma, or iron-depletion, infection induced the genes of CTGF, IL-6, IL-8, IL-11, LIF, EGR-1 and ETV4 in a similar fashion. However, after a longer time, two modes of host-cell reaction emerged that were dependent on the persistence model used. After IFN-gamma and penicillin treatment chlamydia-induced host-cell gene expression was inhibited, while it stayed upregulated in iron-depletion. Human monocytes/macrophages, in which persistence naturally occurs, were additionally investigated: for several genes, UV-inactivated and viable chlamydia caused long-lasting upregulation. Thus, this study reveals (i) the ability of C. pneumoniae to participate in two putative pathomechanisms of persistence, silencing and permanent activation, which might represent different in vivo situations and (ii) a strong dependence on the mode of persistence induction.     

Analysis of gene expression in penicillin G induced persistence of Chlamydia pneumoniae

Chlamydia pneumoniae is responsible for respiratory tract infections and has been associated to chronic diseases such as atherosclerosis. The involvement of C. pneumoniae in chronic diseases may be correlated to its ability to induce persistent forms in which Chlamydiae remain viable but are not cultivable. The aim of our study is to investigate C. pneumoniae specific gene activities associated with the development of Chlamydial persistence in a cell culture system in the presence of penicillin G. Chlamydia-infected HEp 2 cells were incubated with or without penicillin G for up to 72 hours. The relative mRNA expression levels of early and late genes in treated and untreated cell cultures were determined by Real-time RT-PCR. Our results revealed a consistent down-regulation of Chlamydial hctA and hctB genes (p=0.012 and p=0.003 respectively) in association with up-regulation of htrA gene (p=0.002) during penicillin G-induced persistence suggesting these gene sets as leading candidate for in vivo investigation of the development of persistent Chlamydial infection. In conclusion, the Chlamydial expression pattern of hctA, hctB, and htrA genes may be helpful to identify target molecules to diagnose and treat Chlamydia-associated chronic diseases.     

Characterization of a new myrosinase in Brassica napus

A full-length cDNA clone defining the new myrosinase gene family MC in Brassica napus was isolated and sequenced. Southern hybridization showed that the MC family probably consists of 3 or 4 genes in B. napus. MC genes are expressed in the developing seed, but not in the vegetative tissues investigated. In situ hybridizations to developing seeds showed that the MC genes are expressed in the myrosin cells of the embryo axis and the cotyledons. Complexes with myrosinase and myrosinase-binding protein (MBP) were purified and characterized. Sequencing of peptides from myrosinases occurring in the complexes showed that the 70 kDa myrosinase is encoded by the MC genes, whereas the 65 kDa myrosinase is encoded by the MB genes. This is in contrast to the 75 kDa myrosinase which occurs in free form and is encoded by the MA genes. Deglycosylations of the myrosinase complexes and the free myrosinase showed that the molecular sizes of the myrosinases could be reduced significantly by this treatment, and that the size differences between the different myrosinases are mainly due to differences in glycosylation.     

Examination of an inducible expression system for limiting iron availability during Chlamydia trachomatis infection

The obligate intracellular bacterium Chlamydia trachomatis requires iron in order to complete its developmental cycle. Addition of an iron-chelating drug, Desferal (deferoxamine mesylate), to infected cell culture causes Chlamydia to enter persistence. Here, we explore the ability of a stably-transfected cell line with inducible over-expression of the eukaryotic iron efflux protein ferroportin to starve C. trachomatis serovar E for iron. Ferroportin-induced iron removal is perhaps a more direct method of removing iron from the intracellular compartment versus exposure to an exogenous chemical chelator. Following induction, ferroportin-green fluorescent protein (Fpn-GFP) was detected in the plasma membrane, and cells expressing Fpn-GFP remained viable throughout the timescale required for Chlamydia to complete its developmental cycle. Following Fpn-GFP induction in infected cells, chlamydial infectivity remained unchanged, indicating chlamydiae were not in persistence. Ferritin levels indicate only a small decrease in cellular iron following Fpn-GFP expression relative to cultures exposed to Desferal. These data indicate that expression of Fpn-GFP in chlamydiae-infected cells is not capable of reducing iron below the threshold concentration needed to cause chlamydiae to enter persistence.     

Chlamydia muridarum enters a viable but non-infectious state in amoxicillin-treated BALB/c mice

In culture, exposure to penicillin and other stressors induce chlamydiae to enter a non-infectious but viable state termed persistence. Chlamydiae may reenter their normal developmental cycle after stressor removal. Though aberrant RB similar to those present in culture models of persistence have been observed within infected tissues, the existence of persistent chlamydiae has not been definitively demonstrated in vivo. As a result, the role of persistent organisms in pathogenesis is undefined. In order to establish an experimentally tractable model of in vivo persistence, Chlamydia muridarum vaginally-infected mice were gavaged with either water or amoxicillin (amox). Vaginal swabs were collected for chlamydial titration and RNA isolated for quantification of pre-16s rRNA. Uterine tissue was analyzed by transmission electron microscopy (TEM). Although amox-treatment reduced vaginal shedding by >99%, C. muridarum pre-16s rRNA accumulation was unchanged by treatment. These data indicate that the amox-exposed organisms were viable but not infectious. Furthermore, TEM analyses demonstrated that inclusions in amox-treated animals contained primarily large, aberrant RB, but those observed in untreated control animals were normal. Collectively, these data suggest that amoxicillin treatment induces C. muridarum to enter the persistent state in vivo. This model also represents the first experimentally tractable animal model of chlamydial persistence.     

基因工程改良植物重金属抗性与富集能力的研究进展

基于分子水平上对植物吸收、解毒、忍耐以及超富集重金属的几个关键步骤的认识,以及一些功能基因相继在细菌、酵母、植物和动物中被分离、鉴定,近年来,人们利用转基因技术提高植物重金属抗性和富集能力方面已获得进展, 一些功能基因（如gsh1, MerA和ArsC)及其工程植物已显示出植物修复产业化潜力。特别对转基因技术所采取的分子生物学途径、达到的效果以及存在的问题进行了详述,对今后研究的重点和策略进行了探讨。     

Functional genomic studies of tick cells in response to infection with the cattle pathogen, Anaplasma marginale

The coevolution of ticks and the pathogens that they transmit has ensured their mutual survival. In these studies, we used a functional genomics approach to characterize tick genes regulated in response to Anaplasma marginale infection. Differentially regulated genes/proteins were identified by suppression-subtractive hybridization and differential in-gel electrophoresis analyses of cultured IDE8 tick cells infected with A. marginale. Nine of 17 of these genes were confirmed by real-time RT-PCR to be differentially regulated in ticks and/or IDE8 tick cells in response to A. marginale infection. RNA interference was used for functional studies. Six genes, which encode putative selenoprotein W2a, hematopoietic stem/progenitor cells protein-like, proteasome 26S subunit, ferritin, GST, and subolesin control, were found to affect A. marginale infection in IDE8 tick cells. Four genes, which encode putative GST, salivary selenoprotein M, vATPase, and ubiquitin, affected A. marginale infection in different sites of development in ticks. The results of these studies demonstrated that a molecular mechanism occurs by which tick cell gene expression mediates the A. marginale developmental cycle and trafficking through ticks.     

Chlamydia attachment to mammalian cells requires protein disulfide isomerase

For Chlamydia, an intracellular pathogen of humans, host cell invasion is obligatory for survival, growth and pathogenesis. At the molecular level, little is known about the binding and entry of Chlamydia into the mammalian host cell. Chlamydia are genetically intractable therefore experimental approaches targeting the host are often necessary. CHO6 is a mutagenized cell line resistant to attachment and infection by Chlamydia. In this study, CHO6 was shown using proteomic methods to have a defect in processing of the leader sequence for protein disulfide isomerase (PDI). Complementation by expression of full-length PDI restored C. trachomatis binding and infectivity in the CHO6 mutant cell line. The cell line was also resistant to diphtheria toxin and required complemented cell-surface PDI for toxin entry. These data demonstrate that native PDI at the cell surface is required for effective chlamydial attachment and infectivity.     

Gene set enrichment analysis: performance evaluation and usage guidelines

A central goal of biology is understanding and describing the molecular basis of plasticity: the sets of genes that are combinatorially selected by exogenous and endogenous environmental changes, and the relations among the genes. The most viable current approach to this problem consists of determining whether sets of genes are connected by some common theme, e.g. genes from the same pathway are overrepresented among those whose differential expression in response to a perturbation is most pronounced. There are many approaches to this problem, and the results they produce show a fair amount of dispersion, but they all fall within a common framework consisting of a few basic components. We critically review these components, suggest best practices for carrying out each step, and propose a voting method for meeting the challenge of assessing different methods on a large number of experimental data sets in the absence of a gold standard.     

Modelling Chlamydia–koala interactions: coexistence, population dynamics and conservation implications

1. Considerable research has been conducted on koala Phascolarctos cinereus population dynamics and the epidemiology of Chlamydia psittaci infection in koalas, but the impact of Chlamydia on koala populations has been difficult to assess.
2. I developed a model of koala and Chlamydia population dynamics to examine interactions between Chlamydia transmission and pathogenicity, koala mating behaviour and demography, and koala population persistence.
3. Simulations based on sexual and parent–offspring parasite transmission demonstrate that stable Chlamydia–koala coexistence is possible in a small population for a broad range of demographic, behavioural, pathogenicity and transmission parameter estimations. Koala population persistence was most sensitive to reduced annual survivorship of adults (4–10-year-old males and 2–12-year-old females), highlighting the need for accurate field estimates of adult survivorship in order to assess Chlamydia 's impact on specific populations.
4. If koalas become less resistant to disease in fragmented, high-stress habitats (i.e. experience increased Chlamydia -induced mortality and sterility rates), Chlamydia is not predicted to cause koala extinctions under most conditions. Extinctions are only predicted if Chlamydia transmission rates also increase (e.g. due to new transmission pathways or increased mating frequency), or other non-disease factors change birth and mortality rates to reduce the koala population's intrinsic rate of increase below 0·1.
5. The most important predicted effect of habitat fragmentation and other forms of human disturbance on this unique host–parasite relationship is the extinction of Chlamydia in populations where koala resistance to disease decreases.     

Developing salt tolerant plants in a new century: a molecular biology approach

Soil salinity is a major abiotic stress in plant agriculture strongly, influencing plant productivity world-wide. Classical breeding for salt tolerance in crop plants has been attempted to improve field performance without success. Therefore, an alternative strategy is to generate salt tolerant plants through genetic engineering. Several species and experimental approaches have been used in order to identify those genes that are important for salt tolerance. Due to high level of salt tolerance, halophytes are good candidates to identify salt tolerance genes. However, other species such as yeast and glycophytes have also been employed. Three approaches are commonly used to identify genes important for salt tolerance. The first approach is to identify genes involved in processes known to be critical for salt tolerance (osmolyte synthesis, ion homeostasis, etc.). The second approach is to identify genes whose expression is regulated by salt stress. This is relatively simply and applicable to any plant species. Genetic amenability of some species allows the third approach, which consists in the identification of salt tolerance determinants based on functionality. At the moment, there is a large number of reports in the literature claiming that plants with increased salt tolerance have been obtained. The main problem is that different plant species, stage of development, organs, promoters and salt conditions used it is difficult to compare the degree of salt tolerance conferred by different genes. In this review, we discuss progress made towards understanding the molecular elements involved in salt stress responses that have been used in transgenic approaches to improve salt tolerance.     

Identification of a serine protease inhibitor which causes inclusion vacuole reduction and is lethal to Chlamydia trachomatis

The mechanistic details of the pathogenesis of Chlamydia, an obligate intracellular pathogen of global importance, have eluded scientists due to the scarcity of traditional molecular genetic tools to investigate this organism. Here we report a chemical biology strategy that has uncovered the first essential protease for this organism. Identification and application of a unique CtHtrA inhibitor (JO146) to cultures of Chlamydia resulted in a complete loss of viable elementary body formation. JO146 treatment during the replicative phase of development resulted in a loss of Chlamydia cell morphology, diminishing inclusion size, and ultimate loss of inclusions from the host cells. This completely prevented the formation of viable Chlamydia elementary bodies. In addition to its effect on the human Chlamydia trachomatis strain, JO146 inhibited the viability of the mouse strain, Chlamydia muridarum, both in vitro and in vivo. Thus, we report a chemical biology approach to establish an essential role for Chlamydia CtHtrA. The function of CtHtrA for Chlamydia appears to be essential for maintenance of cell morphology during replicative the phase and these findings provide proof of concept that proteases can be targeted for antimicrobial therapy for intracellular pathogens.     

Egg-laying rhythm in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Extensive research has been carried out to understand how circadian clocks regulate various physiological processes in organisms. The discovery of clock genes and the molecular clockwork has helped researchers to understand the possible role of these genes in regulating various metabolic processes. In Drosophila melanogaster, many studies have shown that the basic architecture of circadian clocks is multi-oscillatory. In nature, different neuronal subgroups in the brain of D. melanogaster have been demonstrated to control different circadian behavioural rhythms or different aspects of the same circadian rhythm. Among the circadian phenomena that have been studied so far in Drosophila, the egg-laying rhythm is unique, and relatively less explored. Unlike most other circadian rhythms, the egg-laying rhythm is rhythmic under constant light conditions, and the endogenous or free-running period of the rhythm is greater than those of most other rhythms. Although the clock genes and neurons required for the persistence of adult emergence and activity/rest rhythms have been studied extensively, those underlying the circadian egg-laying rhythm still remain largely unknown. In this review, we discuss our current understanding of the circadian egg-laying rhythm in D. melanogaster, and the possible molecular and physiological mechanisms that control the rhythmic output of the egg-laying process.     

Characterization of the aldehyde dehydrogenase gene families of Zea mays and Arabidopsis

Cytoplasmic male sterility is a maternally transmitted inability to produce viable pollen. Male sterility occurs in Texas (T) cytoplasm maize as a consequence of the premature degeneration of the tapetal cell layer during microspore development. This sterility can be overcome by the combined action of two nuclear restorer genes, rf1 and rf2a. The rf2a gene encodes a mitochondrial aldehyde dehydrogenase (ALDH) that is capable of oxidizing a variety of aldehydes. Six additional ALDH genes were cloned from maize and Arabidopsis. In vivo complementation assays and in vitro enzyme analyses demonstrated that all six genes encode functional ALDHs. Some of these ALDHs are predicted to accumulate in the mitochondria, others in the cytosol. The intron/exon boundaries of these genes are highly conserved across maize and Arabidopsis and between mitochondrial and cytosolic ALDHs. Although animal, fungal, and plant genomes each encode both mitochondrial and cytosolic ALDHs, it appears that either the gene duplications that generated the mitochondrial and the cytosolic ALDHs occurred independently within each lineage or that homogenizing gene conversion-like events have occurred independently within each lineage. All studied plant genomes contain two confirmed or predicted mitochondrial ALDHs. It appears that these mitochondrial ALDH genes arose via independent duplications after the divergence of monocots and dicots or that independent gene conversion-like events have homogenized the mitochondrial ALDH genes in the monocot and dicot lineages. A computation approach was used to identify amino acid residues likely to be responsible for functional differences between mitochondrial and cytosolic ALDHs.     

Expressional profiling study revealed unique expressional patterns and dramatic expressional divergence of maize α-zein super gene family

The α-zein super gene family encodes the most predominant storage protein in maize (Zea mays) endosperm. In maize inbred line B73, it consists of four gene families with 41 member genes. In this study, we combined quantitative real-time PCR and random clone sequencing to successfully profile the expression of α-zein super gene family during endosperm development. We found that only 18 of the 41 member genes were expressed, and their expression levels diverge greatly. At the gene family level, all families had characteristic “up-and-down” oscillating expressional patterns that diverged into two major groups. At the individual gene level, member genes showed dramatic divergence of expression patterns, indicating fast differentiation of their expression regulation. A comparison study among different inbred lines revealed significantly different expressed gene sets, indicating the existence of highly diverged haplotypes. Large gene families containing long gene clusters, e.g. z1A or z1C, mainly contributed the highly divergent haplotypes. In addition, allelic genes also showed significant divergence in their expressional levels. These results indicated a highly dynamic and fast evolving nature to the maize α-zein super gene family, which might be a common feature for other large gene families. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Lingna Feng and Jia Zhu contributed equally to this work.     

The persistence of bifidobacteria populations in a river measured by molecular and culture techniques

Aims:  To determine relative to faecal coliforms (FC) and sulfite-reducing clostridia (SRC), the environmental persistence of natural populations of Bifidobacterium spp. enumerated by culturing and quantitative polymerase chain reaction (q-PCR).
Methods and Results:  Dialysis tubing containing river supplemented with overnight cultures of Bifidobacterium adolescentis (BA) and Bifidobacterium dentium (BD) or urban wastewater were suspended in a river for up to 10 days. At intervals, the contents of each dialysis tube were assayed using q-PCR assays for BA and BD, and selective culture media for FC, SRC, total bifidobacteria (TB), sorbitol-fermenting bifidobacteria (SFB) and cultivable BA. Mean summer T ₉₀ values were 251 h for SRC, 92 h for FC, 48 h for BA and BD by q-PCR, and 9 h for TB.
Conclusions:  Bifidobacterium spp. was the population with the lowest persistence, showing seasonal differences in T ₉₀ when measured by culture techniques or by q-PCR. This difference in relative persistence is because of a longer persistence of molecular targets than cultivable cells.
Significance and Impact of the Study:  The persistence of a viable bifidobacteria cells is shorter, but the longest persistence of molecular targets. This factor could be used for origin the faecal pollution in water for the development of microbial source tracking (MST).     

Relative developmental, environmental, and tree-to-tree variability in buds from field-grown apple trees

High-throughput genomic technologies are becoming more accessible to nonmodel plant species, and therefore, tissue collected outside controlled environments is being increasingly used for microarray analyses. In this study, we present a 15,720-feature apple microarray analysis of the variability of gene expression in buds from field-grown apple trees. Tree-to-tree and day-to-day variances were assessed during two different seasons: summer, when the meristems in the buds were undergoing the first stages of floral development, and autumn, when the buds were undergoing transition to winter dormancy. We found that apple trees with the same scion and rootstock cultivars, grown in a standard orchard environment, had small tree-to-tree variation. Gene expression differences caused by season was the dominant cause of variance while using false discovery rate control with a threshold of α* = 0.01 to select significantly different expression between genes. At this threshold, the environmental and location effects accounted for less than 10% of the genes selected. Consequently, we have shown that field microarray experiments are a viable approach for measuring seasonal changes in gene expression during apple bud development. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.