Exploiting interactions among polymorphisms contributing to complex disease traits with boosted generative modeling.

Although there has been great success in identifying disease genes for simple, monogenic Mendelian traits, deciphering the genetic mechanisms involved in complex diseases remains challenging. One major approach is to identify configurations of interacting factors such as single nucleotide polymorphisms (SNPs) that confer susceptibility to disease. Traditional methods, such as the multiple dimensional reduction method and the combinatorial partitioning method, provide good tools to decipher such interactions amid a disease population with a single genetic cause. However, these traditional methods have not managed to resolve the issue of genetic heterogeneity, which is believed to be a very common phenomenon in complex diseases. There is rarely prior knowledge of the genetic heterogeneity of a disease, and traditional methods based on estimation over the entire population are unlikely to succeed in the presence of heterogeneity. We present a novel Boosted Generative Modeling (BGM) approach for structure-model the interactions leading to diseases in the context of genetic heterogeneity. Our BGM method bridges the ensemble and generative modeling approaches to genetic association studies under a case-control design. Generative modeling is employed to model the interaction network configuration and the causal relationships, while boosting is used to address the genetic heterogeneity problem. We perform our method on simulation data of complex diseases. The results indicate that our method is capable of modeling the structure of interaction networks among disease-susceptible loci and of addressing genetic heterogeneity issues where the traditional methods, such as multiple dimensional reduction method, fail to apply. Our BGM method provides an exploratory tool that identifies the variables (e.g., disease-susceptible loci) that are likely to correlate and contribute to the disease.     

An atypical mitogen-activated protein kinase (MAPK) homologue expressed in gametocytes of the human malaria parasite Plasmodium falciparum. Identification of a MAPK signature.

The cDNA encoding Pfmap-2, an enzyme of the human malaria parasite Plasmodium falciparum, was cloned, sequenced, and expressed in Escherichia coli. The open reading frame carried by the Pfmap-2 cDNA encodes a 508-amino acid polypeptide of 59.2 kDa with maximal homology to mitogen-activated protein kinases (MAPKs) from various organisms. The purified recombinant enzyme displayed functional characteristics of MAPKs such as (i) ability to undergo autophosphorylation, (ii) ability to phosphorylate myelin basic protein, a classical MAPK substrate, (iii) regulation of kinase activity by a MAPK-specific phosphatase, and (iv) ability to be activated by component(s) present in cell extracts. Mutational analysis of the recombinant protein allowed the identification of residues that are important for enzymatic activity. Northern blot analysis and immunofluorescence assays indicated that Pfmap-2 is expressed specifically in gametocytes, the form that is responsible for transmission of the parasite to the mosquito vector. Gametocyte extracts activated recombinant Pfmap-2 more efficiently than extracts from asexual parasites, which is consistent with this stage specificity. Despite its overall high level of homology to MAPKs, Pfmap-2 presents the peculiarity of not possessing the conserved threonine-X-tyrosine activation motif usually found in enzymes of this family; instead, it has a threonine-serine-histidine at the same location. This atypical feature formed the basis for a detailed analysis of the primary structure of MAPKs, allowing us to define an operational MAPK signature, which is shared by Pfmap-2. The fact that no MAPK from vertebrates diverge in the activation motif suggests that the fine mechanisms of Pfmap-2 regulation may offer an opportunity for antimalarial drug targeting.     

The Effects Of Short Time Right Ventricular Pacing On Left Atrial Mechanical Functions

Objectives

Left atrium (LA) plays an important role in left ventricular filling. It is well known that right ventricular apical pacing has unfavorable effects on ventricular systolic and diastolic performance. The aim of this study is to evaluate the LA mechanical functions with 2D echocardiography in patients with a permanent pacemaker after short time ventricular pacing.

Design

Echocardiographic examination was performed in 38 patients (mean age 63.0± 10.9, 18 female) with dual chamber pacemakers or defibrillators (< 20% ventricular pacing within previous 6 months, all of them on sinus rhythm) before and after 4 hours > 90% ventricular pacing at 70 beats per minute in DDD mode with an optimal AV interval. Left atrial volumes (LAV) including at the time of mitral valve opening (Vmax), at closure (Vmin), and at the onset of atrial systole (Volp) were measured. The passive emptying, conduit, active emptying and total emptying volume, stroke volumes were also calculated.

Results

No significant differences were noted at baseline and after pacing for absolute Vmax, Volp, passive emptying, conduit, active emptying, total emptying volumes as well as the volumes indexed to body surface area (p >0.05).

Conclusions

Short - time RV pacing seems to have no acute effects on left atrial mechanical functions.     

Evolution unbound: releasing the arrow of complexity

The common opinion has been that evolution results in the continuing development of more complex forms of life, generally understood as more complex organisms. The arguments supporting that opinion have recently come under scrutiny and been found wanting. Nevertheless, the appearance of increasing complexity remains. So, is there some sense in which evolution does grow complexity? Artificial life simulations have consistently failed to reproduce even the appearance of increasing complexity, which poses a challenge. Simulations, as much as scientific theories, are obligated at least to save the appearances! We suggest a relation between these two problems, understanding biological complexity growth and the failure to model even its appearances. We present a different understanding of that complexity which evolution grows, one that genuinely runs counter to entropy and has thus far eluded proper analysis in information-theoretic terms. This complexity is reflected best in the increase in niches within the biosystem as a whole. Past and current artificial life simulations lack the resources with which to grow niches and so to reproduce evolution??s complexity. We propose a more suitable simulation design integrating environments and organisms, allowing old niches to change and new ones to emerge.     

Comparison of liposome entrapment parameters by optical and atomic absorption spectrophotometry

Methods for the complete characterization of liposomes prepared by ether-injection are described in detail. The validity of atomic absorption spectrophotometry Ior measuring markers of trapped volume was checked by comparative determinations of markers with established optical spectrophotometrical methods. The favorable results usingl atomic absorption spectrophotometry to quantitate the marker Mn²⁺ are of particular relevance as manganese ion is also the paramagnetic probe in n.m.r, measurements of water permeability of lipo-somes; our results indicate that in such measurements no other marker need be incorporated.     

Quinolinic Acid Amyloid-like Fibrillar Assemblies Seed α-Synuclein Aggregation

Quinolinic acid (QA), a downstream neurometabolite in the kynurenine pathway, the biosynthetic pathway of tryptophan, is associated with neurodegenerative diseases pathology. Mutations in genes encoding kynurenine pathway enzymes, which control the level of QA production, are linked with elevated risk of developing Parkinson's disease. Recent findings have revealed the accumulation and deposition of QA in post-mortem samples, as well as in cellular models of Alzheimer's disease and related disorders. Furthermore, intrastriatal inoculation of mice with QA results in increased levels of phosphorylated α-synuclein and neurodegenerative pathological and behavioral characteristics. However, the cellular and molecular mechanisms underlying the involvement of QA accumulation in protein aggregation and neurodegeneration remain elusive. We recently established that self-assembled ordered structures are formed by various metabolites and hypothesized that these “metabolite amyloids” may seed amyloidogenic proteins. Here we demonstrate the formation of QA amyloid-like fibrillar assemblies and seeding of α-synuclein aggregation by these nanostructures both in vitro and in cell culture. Notably, α-synuclein aggregation kinetics was accelerated by an order of magnitude. Additional amyloid-like properties of QA assemblies were demonstrated using thioflavin T assay, powder X-ray diffraction and cell apoptosis analysis. Moreover, fluorescently labeled QA assemblies were internalized by neuronal cells and co-localized with α-synuclein aggregates. In addition, we observed cell-to-cell propagation of fluorescently labeled QA assemblies in a co-culture of treated and untreated cells. Our findings suggest that excess QA levels, due to mutations in the kynurenine pathway, for example, may lead to the formation of metabolite assemblies that seed α-synuclein aggregation, resulting in neuronal toxicity and induction of Parkinson's disease.     

Toxicity and tolerance of aluminum in plants: tailoring plants to suit to acid soils

Aluminum (Al) stress is one of the serious limiting factors in plant productivity in acidic soils, which constitute about 50 % of the world’s potentially arable lands and causes anywhere between 25 and 80 % of yield losses depending upon the species. The mechanism of Al toxicity and tolerance has been examined in plants, which is vital for crop improvement and enhanced food production in the future. Two mechanisms that facilitate Al tolerance in plants are Al exclusion from the roots and the ability to tolerate Al in the symplast or both. Although efforts have been made to unravel Al-resistant factors, many aspects remain unclear. Certain gene families such as MATE, ALMT, ASR, and ABC transporters have been implicated in some plants for resistance to Al which would enhance the opportunities for creating crop plants suitable to grow in acidic soils. Though QTLs have been identified related to Al-tolerance, no crop plant that is tolerant to Al has been evolved so far using breeding or molecular approaches. The remarkable changes that plants experience at the physiological, biochemical and molecular level under Al stress, the vast array of genes involved in Al toxicity-tolerance, the underlying signaling events and the holistic image of the molecular regulation, and the possibility of creating transgenics for Al tolerance are discussed in this review.     

An Anti-β-Amyloid Vaccine for Treating Cognitive Deficits in a Mouse Model of Down Syndrome

In Down syndrome (DS) or trisomy of chromosome 21, the β-amyloid (Aβ) peptide product of the amyloid precursor protein (APP) is present in excess. Evidence points to increased APP gene dose and Aβ as playing a critical role in cognitive difficulties experienced by people with DS. Particularly, Aβ is linked to the late-life emergence of dementia as associated with neuropathological markers of Alzheimer’s disease (AD). At present, no treatment targets Aβ–related pathogenesis in people with DS. Herein we used a vaccine containing the Aβ 1–15 peptide embedded into liposomes together with the adjuvant monophosphoryl lipid A (MPLA). Ts65Dn mice, a model of DS, were immunized with the anti-Aβ vaccine at 5 months of age and were examined for cognitive measures at 8 months of age. The status of basal forebrain cholinergic neurons and brain levels of APP and its proteolytic products were measured. Immunization of Ts65Dn mice resulted in robust anti-Aβ IgG titers, demonstrating the ability of the vaccine to break self-tolerance. The vaccine-induced antibodies reacted with Aβ without detectable binding to either APP or its C-terminal fragments. Vaccination of Ts65Dn mice resulted in a modest, but non-significant reduction in brain Aβ levels relative to vehicle-treated Ts65Dn mice, resulting in similar levels of Aβ as diploid (2N) mice. Importantly, vaccinated Ts65Dn mice showed resolution of memory deficits in the novel object recognition and contextual fear conditioning tests, as well as reduction of cholinergic neuron atrophy. No treatment adverse effects were observed; vaccine did not result in inflammation, cellular infiltration, or hemorrhage. These data are the first to show that an anti-Aβ immunotherapeutic approach may act to target Aβ-related pathology in a mouse model of DS.     

Cystic fibrosis--the way forward from the gene.

Cloning of the cystic fibrosis (CF) gene and elucidation of the physiological functions of the encoded protein is a triumph, not only for molecular biology, but also for people affected by CF. For them, not only is there now the possibility of screening for the commonest mutations, but they may also look forward to the prospect of improved therapies being developed.