The Hsp90–Sti1 interaction is critical for Leishmania donovani proliferation in both life cycle stages

The heat shock protein 90 plays a pivotal role in the life cycle control of Leishmania donovani promoting the fast‐growing insect stage of this parasite. Equally important for insect stage growth is the co‐chaperone Sti1. We show that replacement of Sti1 is only feasible in the presence of additional Sti1 transgenes indicating an essential role. To better understand the impact of Sti1 and its interaction with Hsp90, we performed a mutational analysis of Hsp90. We established that a single amino acid exchange in the Leishmania Hsp90 renders that protein resistant to the inhibitor radicicol (RAD), yet does not interfere with its functionality. Based on this RAD‐resistant Hsp90, we established a combined chemical knockout/gene complementation (CKC) approach. We can show that Hsp90 function is required in both insect and mammalian life stages and that the Sti1‐binding motif of Hsp90 is crucial for proliferation of insect and mammalian stages of the parasite. The Sti1‐binding motif in Leishmania Hsp90 is suboptimal – optimizing the motif increased initial intracellular proliferation underscoring the importance of the Hsp90–Sti1 interaction for this important parasitic protozoan. The CKC strategy we developed will allow the future analysis of more Hsp90 domains and motifs in parasite viability and infectivity.     

PRISE2: Software for designing sequence-selective PCR primers and probes

Background

PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3’ end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines.

Results

PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays.

Conclusions

PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.     

Promoter hypermethylation using 24-gene array in early head and neck cancer: Better outcome in oral than in oropharyngeal cancer

Silencing of tumor suppressor genes (TSGs) by DNA promoter hypermethylation is an early event in carcinogenesis and a potential target for personalized cancer treatment. In head and neck cancer, little is known about the role of promoter hypermethylation in survival. Using methylation specific multiplex ligation-dependent probe amplification (MS-MLPA) we investigated the role of promoter hypermethylation of 24 well-described genes (some of which are classic TSGs), which are frequently methylated in different cancer types, in 166 HPV-negative early oral squamous cell carcinomas (OSCC), and 51 HPV-negative early oropharyngeal squamous cell carcinomas (OPSCC) in relation to clinicopathological features and survival. Early OSCC showed frequent promoter hypermethylation in RARB (31% of cases), CHFR (20%), CDH13 (13%), DAPK1 (12%), and APC (10%). More hypermethylation (≥ 2 genes) independently correlated with improved disease specific survival (hazard ratio 0.17, P = 0.014) in early OSCC and could therefore be used as prognostic biomarker. Early OPSCCs showed more hypermethylation of CDH13 (58%), TP73 (14%), and total hypermethylated genes. Hypermethylation of two or more genes has a significantly different effect on survival in OPSCC compared with OSCC, with a trend toward worse instead of better survival. This could have a biological explanation, which deserves further investigation and could possibly lead to more stratified treatment in the future.     

Theta Dynamics in Rat: Speed and Acceleration across the Septotemporal Axis

Theta (6–12 Hz) rhythmicity in the local field potential (LFP) reflects a clocking mechanism that brings physically isolated neurons together in time, allowing for the integration and segregation of distributed cell assemblies. Variation in the theta signal has been linked to locomotor speed, sensorimotor integration as well as cognitive processing. Previously, we have characterized the relationship between locomotor speed and theta power and how that relationship varies across the septotemporal (long) axis of the hippocampus (HPC). The current study investigated the relationship between whole body acceleration, deceleration and theta indices at CA1 and dentate gyrus (DG) sites along the septotemporal axis of the HPC in rats. Results indicate that whole body acceleration and deceleration predicts a significant amount of variability in the theta signal beyond variation in locomotor speed. Furthermore, deceleration was more predictive of variation in theta amplitude as compared to acceleration as rats traversed a linear track. Such findings highlight key variables that systematically predict the variability in the theta signal across the long axis of the HPC. A better understanding of the relative contribution of these quantifiable variables and their variation as a function of experience and environmental conditions should facilitate our understanding of the relationship between theta and sensorimotor/cognitive functions.     

DNA methylation of IGF2, GNASAS,INSIGF and LEP and being born small for gestational age

Being born small for gestational age (SGA), a proxy for intrauterine growth restriction (IUGR) and prenatal famine exposure are both associated with a greater risk of metabolic disease. Both associations have been hypothesized to involve epigenetic mechanisms. We investigated whether prenatal growth restriction early in pregnancy was associated with changes in DNA methylation at loci that were previously shown to be sensitive to early gestational famine exposure. We compared 38 individuals born preterm (<32 weeks) and with a birth weight too low for their gestational age (less than −1SDS; SGA) with 75 individuals born preterm but with a birth weight appropriate for their gestational age (greater than −1SDS) and a normal postnatal growth (greater than −1SDS at three months post term; AGA). The SGA individuals were not only lighter at birth, but also had a smaller length (p = 3.3 × 10⁻¹³) and head circumference at birth (p = 4.1 × 10⁻¹³). The DNA methylation levels of IGF2, GNASAS, INSIGF and LEP were 48.5, 47.5, 79.4 and 25.7% respectively. This was not significantly different between SGA and AGA individuals. Risk factors for being born SGA, including preeclampsia and maternal smoking, were also not associated with DNA methylation at these loci. Growth restriction early in development is not associated with DNA methylation at loci shown to be affected by prenatal famine exposure. Our and previous results by others indicate that prenatal growth restriction and famine exposure may be associated with different epigenetic changes or non-epigenetic mechanisms that may lead to similar later health outcomes.Key words: SGA, DOHAD, IUGR, DNA methylation, famine, IGF2, LEP, INS, GNASAS     

Persistent spatial working memory deficits in rats following in utero RNAi of Dyx1c1

Disruptions in the development of the neocortex are associated with cognitive deficits in humans and other mammals. Several genes contribute to neocortical development, and research into the behavioral phenotype associated with specific gene manipulations is advancing rapidly. Findings include evidence that variants in the human gene DYX1C1 may be associated with an increased risk of developmental dyslexia. Concurrent research has shown that the rat homolog for this gene modulates critical parameters of early cortical development, including neuronal migration. Moreover, recent studies have shown auditory processing and spatial learning deficits in rats following in utero transfection of an RNA interference (RNAi) vector of the rat homolog Dyx1c1 gene. The current study examined the effects of in utero RNAi of Dyx1c1 on working memory performance in Sprague-Dawley rats. This task was chosen based on the evidence of short-term memory deficits in dyslexic populations, as well as more recent evidence of an association between memory deficits and DYX1C1 anomalies in humans. Working memory performance was assessed using a novel match-to-place radial water maze task that allows the evaluation of memory for a single brief (～4-10 seconds) swim to a new goal location each day. A 10-min retention interval was used, followed by a test trial. Histology revealed migrational abnormalities and laminar disruption in Dyx1c1 RNAi-treated rats. Dyx1c1 RNAi-treated rats exhibited a subtle, but significant and persistent impairment in working memory as compared to Shams. These results provide further support for the role of Dyx1c1 in neuronal migration and working memory.     

Adult AIDS-Like Disease in a Novel Inducible Human Immunodeficiency Virus Type 1 Nef Transgenic Mouse Model: CD4+ T-Cell Activation Is Nef Dependent and Can Occur in the Absence of Lymphophenia

CD4C/HIV^nef transgenic (Tg) mice express Nef in CD4⁺ T cells and in the cells of the macrophage/monocyte/dendritic lineage, and they develop an AIDS-like disease similar to human AIDS. In these mice, Nef is constitutively expressed throughout life. To rule out the contribution of any developmental defects caused by early expression of Nef, we generated inducible human immunodeficiency virus type 1 (HIV-1) Nef Tg mice by using the tetracycline-inducible system. Faithful expression of the Nef transgene was induced in (CD4C/rtTA × TRE/HIV^Nef) or (CD4C/rtTA2^S-M2 × TRE/HIV^Nef) double-Tg mice upon doxycycline (DOX) treatment in drinking water. Long-term treatment of these mice with DOX also led to loss, apoptosis, and activation of CD4⁺ T cells, this latter phenotype being observed even with low levels of Nef. These phenotypes could be transferred by bone marrow (BM) transplantation, indicating a hematopoietic cell autonomous effect. In addition, in mixed Tg:non-Tg BM chimeras, only Tg and not non-Tg CD4⁺ T cells exhibited an effector/memory phenotype in the absence of lymphopenia. Finally, the DOX-induced double-Tg mice developed nonlymphoid organ diseases similar to those of CD4C/HIV^Nef Tg mice and of humans infected with HIV-1. These results show for the first time that adult mice are susceptible to the detrimental action of Nef and that Nef-mediated T-cell activation can be independent of lymphopenia. These Tg mice represent a unique model which is likely to be instrumental for understanding the cellular and molecular pathways of Nef action as well as the main characteristics of immune reconstitution following DOX withdrawal.Small animal models able to express the entire human immunodeficiency virus (HIV) genome or selected HIV genes have provided useful information on the pathogenesis of AIDS and still represent important research tools toward this goal. Among these models, transgenic (Tg) mice containing intact copies of HIV DNA, defective provirus with the gag and pol genes deleted, or individual HIV-1 genes have been reported to develop various pathologies, some of which resemble those found in human AIDS (2, 3, 8, 9, 16, 17, 18, 24, 27, 29, 30, 38, 44, 45, 46, 49, 51, 52). The cell type context in which the HIV-1 transgene is expressed in these Tg mice appears to play an important role in determining the type of pathological lesions. Tg mice generated in our laboratory and expressing the entire coding sequence of HIV-1 (CD4C/HIV^WT) or HIV-1 Nef alone (CD4C/HIV^Nef) in the relevant target cells of HIV-1, namely, CD4⁺ T cells, macrophages, and dendritic cells, develop pathologies very similar to those in human AIDS (17, 18). The AIDS-like disease of CD4C/HIV^Nef Tg mice is characterized by immunodeficiency, loss of CD4⁺ T cells, thymic atrophy, activation of T cells and pathologies in heart, lungs, and kidneys (18, 53). Similarly, expression of simian immunodeficiency virus (SIV) Nef in Tg mice under the control of the same promoter sequences (CD4C) results in an AIDS-like disease (42). These studies demonstrated that Nef plays an important role in the development of the AIDS-like disease induced by HIV-1 or SIV in Tg mice.Among the AIDS-like phenotypes of these models, the T-cell activation observed by a number of groups in Tg mice expressing Nef (3, 33, 44, 53) may be of special interest for its resemblance to that of humans or macaques infected with HIV-1 or SIV, respectively. HIV infection results in a state of chronic immune activation which correlates very closely with disease progression in humans (11, 14, 23). Similarly, SIV-infected macaques which develop AIDS show aberrant immune activation (35), while SIV-infected sooty mangabey monkeys, natural hosts of SIV, do not develop immunopathologies and do not show immune activation either (41). Various factors may contribute to this immune activation, including increased plasma lipopolysaccharide levels due to microbial translocation from the gut (4), impaired regulatory T cell function (32), or the action of the HIV-1 gene products themselves, such as Env gp120 and Nef (10, 12, 43). Consistent with this latter scenario, we reported that in CD4C/HIV^Nef Tg mice the extent of T-cell activation correlates with levels of Nef expression in CD4⁺ T cells, thus suggesting a direct involvement of Nef in this activation (53). In contrast, Koenen and coworkers reported that T-cell activation in CD2/Nef Tg mice is induced indirectly by lymphophenia (26). In that study, chimeric mice, which were generated from a mixture of non-Tg and Nef Tg bone marrow (BM) cells, were not lymphopenic, and the donor-derived Nef-expressing Tg T cells did not show an activated phenotype. However, the donor Nef Tg T cells constituted only 1 to 2% of peripheral T cells of these chimeric mice (26). Clearly, alternative experimental approaches are needed to study this phenotype in a more physiological context.In the previously described CD4C/HIV^Nef Tg mice (18), Nef expression begins early in life and is constitutively expressed throughout the life of the animal. The AIDS-like disease caused by this early expression of Nef best represents a model for pediatric AIDS. However, in these Tg mice, Nef may interfere with normal developmental processes and these latter defects may contribute to some of the phenotypes observed. To assess the effects of Nef in fully mature adult animals, and thus develop a model of adult AIDS, temporal regulation of Nef expression in adult mice using an inducible system is required.In the present study, we chose the tet-On (rtTA and rtTA2^S-M2) system (13, 15, 25, 48) to induce expression of HIV-1 Nef in CD4⁺ T cells and cells of the macrophage/dendritic lineage of mice using the CD4C tissue-specific regulatory elements. These CD4C sequences were previously used to generate the constitutively Nef-expressing CD4C/HIV^Nef Tg mice (18). These inducible adult (TRE/HIV^Nef × CD4C/rtTA) and (TRE/HIV^Nef × CD4C/rtTA2^S-M2) double-Tg (DTg) mice express Nef when treated with doxycycline (DOX) and develop an AIDS-like disease very similar to that seen in constitutively Nef-expressing CD4C/HIV^Nef Tg mice. We took advantage of this novel biological system to reassess the role of Nef in T-cell activation. Using a mixed chimera made with BM cells from these inducible Nef Tg mice and from non-Tg mice, we could document CD4⁺ T-cell activation only in donor-derived Nef-expressing Tg cells, but not in non-Tg cells, in the absence of lymphopenia. This result strongly suggests that this CD4⁺ T-cell activation phenotype is most likely driven by expression of Nef in these cells.     

Medical bioremediation of age-related diseases

Catabolic insufficiency in humans leads to the gradual accumulation of a number of pathogenic compounds associated with age-related diseases, including atherosclerosis, Alzheimer's disease, and macular degeneration. Removal of these compounds is a widely researched therapeutic option, but the use of antibodies and endogenous human enzymes has failed to produce effective treatments, and may pose risks to cellular homeostasis. Another alternative is "medical bioremediation," the use of microbial enzymes to augment missing catabolic functions. The microbial genetic diversity in most natural environments provides a resource that can be mined for enzymes capable of degrading just about any energy-rich organic compound. This review discusses targets for biodegradation, the identification of candidate microbial enzymes, and enzyme-delivery methods.