The Synaptic Leap

 The world’s first open-science unconferencePosted by timo to scibar scifoo on Wed Nov 18 2009 at 10:24 UTC | info | related

 Science Foo Camp 2009Bertalan MeskóScienceRoll, (08 Jul 2009)Posted by timo and 1 other to scifoo09 scifoo on Sun Oct 18 2009 at 12:41 UTC | info | related

The helminth fluorescent bioassay: An objective tool for quantifying schistosome viability.

Confocal microscopy of Schistosoma mansoni schistosomula illustrates the ease by which dead (propidium iodide-positive, red individuals) and live (fluorescein diacetate-positive, green individuals) parasites can be distinguished using a helminth fluorescent bioassay (HFB) described by Peak et al. (doi:10.1371/journal.pntd.1000759). It is anticipated that the HFB will be useful in objectively measuring schistosome survival during immunological assays (antibody- or complement-mediated killing), RNAi investigations, and drug screening protocols.

Image Credit: Emily Peak

Author Summary

Filarial diseases affect over 150 million people in tropical countries. They are caused by parasitic nematodes like Brugia malayi that rely on their endosymbiont Wolbachia for their survival and fertility. These bacteria are a recognized drug target in the search for treatments killing adult worms. To understand the transmission of Wolbachia from the embryonic to adult stages, we developed new techniques to track these bacteria at the cellular and tissue levels. These techniques include immunofluorescence in whole mount adult tissues and embryos. We found that Wolbachia segregate asymetrically in specific cells, in a lineage-specific manner during early Brugia embryogenesis, and rely on cell fusion to subsequently populate the adult hypodermal chords. From the chords, the Wolbachia can be secreted in the secretory-excretory canal, suggesting that in addition to dead worms releasing the bacteria in the human body, living worms may also secrete Wolbachia, whose role in stimulating the immune system in filarial pathologies is now well established.

Author Summary

With only one effective drug, praziquantel, currently used to treat most worldwide cases of schistosomiasis, there exists a pressing need to identify alternative anthelmintics before the development of praziquantel-resistant schistosomes removes our ability to combat this neglected tropical disease. At present, the most widely adopted methodology used to identify promising new anti-schistosome compounds relies on time consuming and subjective microscopic examination of parasite viability in response to in vitro schistosome/compound co-culturing. In our continued effort to identify novel drug and vaccine targets, we detail a dual-fluorescence bioassay that can objectively be used for assessing Schistosoma mansoni schistosomula viability in a medium or high- throughput manner to suit either academic or industrial settings. The described methodology replaces subjectivity with sensitivity and provides an enabling technology useful for rapid in vitro screens of both natural and synthetic compound libraries. It is expected that results obtained from these quantifiable in vitro screens would prioritize the most effective anti-schistosomal compounds for follow-up in vivo experimentation. This highly-adaptable dual-fluorescence bioassay could be integrated with other methods for measuring schistosome phenotype and, together, be used to greatly accelerate our search for novel anthelmintics.

Author Summary

Neglected Tropical Diseases (NTDs) have been targeted due to their prevalence and the burden of disease they cause globally, but there has been no significant focus in the literature on the subject of NTDs as a group in immigrants and travelers, and no specific studies on the emerging phenomenon of imported NTDs. We present the experience of a Tropical Medicine Unit in a major European city, over a 19-year period, describing and comparing NTDs diagnosed amongst immigrants, travelers and travelers visiting friends and relatives (VFRs). NTDs were diagnosed outside tropical areas and occurred more frequently in immigrants, followed by VFR travelers and then by other travelers. The main NTDs diagnosed in immigrants were onchocerciasis, Chagas disease and ascariasis; most frequent NTDs in travelers were schistosomiasis, onchocerciasis and ascariasis, and onchocerciasis and schistosomiasis in VFRs. Issues focusing on modes of transmission outside endemic areas and how eradication programs for some NTDs in endemic countries may have an impact in non-tropical Western countries by decreasing disease burden in immigrants, are addressed. Adherence to basic precautions such as safe consumption of food/water and protection against arthropod bites could help prevent many NTDs in travelers.

Author Summary

Rift Valley fever (RVF) is a disease transmitted by a mosquito bite (Aedes). Humans can also be infected through direct contact with blood (aerosols) or tissues (placenta, stillborn) of infected animals. Although severe clinical cases can be observed, infection with RVF virus (RVFV) in humans in most cases causes a febrile illness without serious symptoms. In small ruminants RVFV mainly causes abortion and neonatal death. RVFV distribution has been poorly investigated in Central Africa. We conducted a large scale serological survey of RVF antibodies in rural populations in Gabon, involving 4,323 individuals from 212 randomly selected villages. The results showed an overall RVFV prevalence of 3.3%, with values of 2.9% in the forested zones, 2.2% in savannas and 8.3% in the lakes region. These findings strongly suggest for the first time the wide circulation of Rift valley fever virus in Gabon and the possible existence of a sylvan cycle of RVF virus in this country. The serological higher prevalence in the lake region suggests that this region is likely to have particular ecological conditions, especially mosquito vector species, favoring the circulation of this virus. In Gabon, human cases of RVF may occur but are either misdiagnosed or not reported.

Author Summary

Visceral leishmaniasis (VL) is a potentially fatal disease without treatment, characterized by prolonged fever, enlargement of spleen and liver, anaemia and weight loss. Treatment for VL is difficult, as it requires prolonged and painful application of toxic drugs with adverse side effects. It is therefore important to develop alternative satisfactory therapies for VL. Herein, we report the efficacy of a new liposomal formulation of amphotericin-B, Fungisome, and the immunological changes that take place 1-week after treatment. Patients treated with 5 and 7.5 mg/kg (single-dose) and 10 mg/kg (5 mg/kg double-dose) of Fungisome showed 60%, 50% and 90% successful cure at 6-month posttreatment, respectively. Successfully cured patients showed reduced IL-12 and IL-10 levels in the plasma and two-fold or more increase in Th1 type-cytokines IFN-γ, IL-12 and TNF, and down-regulation of immunosuppressive factors IL-10 and TGF-β in the culture supernatants, 1-week after treatment independent of drug-dose. Insignificant decrease of plasma IL-12 and IL-10, negligible increase of Th1-cytokines, and persistence of IL-10, despite decrease in TGF-β in culture supernatants, correlated with relapse within 6-months of treatment. These interesting results pave the way for further testing of this drug as a new alternative in the chemotherapy of leishmaniasis.

Author Summary

Dengue virus (DENV) is the cause of the most common vector-borne viral disease of humans, and is at particularly high prevalence in parts of Southeast Asia. Most studies of DENV transmission have focused on very local or international movement patterns, and have not explored how DENV moves through an endemic region. To address this issue, we employed newly developed phylogeographic methods to study patterns of spatial spread in 168 full-length DENV-2 genome sequences collected during a hospital-based study in southern Viet Nam, focusing on the Asian I genotype that recently emerged in this region. This analysis revealed that the urban population of Ho Chi Minh City plays a central role in the dispersal of the virus, and that DENV in this city tends to move along a gradient of population density. In addition, human movement between urban and rural areas was the most likely explanation for the rapid diffusion of DENV across southern Viet Nam following its introduction into Ho Chi Minh City. After reaching more rural areas, some virus lineages were maintained there for a number of years. These results therefore indicate that virological surveillance is necessary in both urban and rural populations.

Author Summary

Snake bite threatens millions of poor rural folk throughout Africa. In Nigeria, as in many countries of sub-Saharan Africa, it takes a terrible toll on human life and limb. Over the years, the news for those exposed to snake bite has been generally bad: withdrawal of antivenom manufacturers, increasing cost and, most recently, the marketing of ineffective or fake antivenoms in the region. Our paper reports encouraging results achieved by two antivenoms created as a direct consequence of the present crisis in antivenom supply for Africa. They have been assessed in the most powerful trial ever attempted in this field. The trial showed that in people with non-clotting blood following carpet viper bite, the commonest cause of snake bite morbidity and mortality in the West African savannah, administration of the antivenoms- EchiTAb G and EchiTAb Plus-ICP led to permanent restoration of blood clotting in 76% and 83% of the patients within 6 hours, respectively. Generally mild early adverse reactions were recorded in 19% and 26%, respectively. Both antivenoms proved effective and acceptably safe and can be recommended for treating carpet viper envenoming in Nigeria.

Making solubility estimations for most organic compounds in a wide range of solvents freely available has always been a main long term objective for the Open Notebook Science Solubility Challenge. With current expertise and technology, it should be as easy to obtain a solubility estimate as it is now to get driving directions off the web.
Obviously this won't be attained purely by exhaustive measurements, although we have been focused on strategic measurements over the past two years. In parallel, we have been constantly evaluating the various solubility models out there for suitability.
Although there are several solubility models available for non-aqueous solvents, our additional requirement for transparent model building has proved surprisingly difficult to satisfy.
From this search, the Abraham solubility model [Abraham2009] floated to the top, with an important factor being that Abraham has made available extensive compilations of descriptors for solutes and solvents. In addition the algorithms used to convert solubility measurements to Abraham descriptors (a minimum of 5 different solvents per solute) has allowed us to generate our own Abraham descriptors automatically simply by recording new measurements into our SolSum Google Spreadsheet. These can be obtained in real time as well.
This approach permitted us to provide predictions for a limited number of solutes in a wide range of solvents and we have included these predictions in the past two editions (2nd and 3rd) of the ONS Challenge Solubility Book.
Coming at the problem from a different approach, Andrew Lang has also been trying to predict solubility using only open molecular descriptors, mainly relying on the CDK. Since our most commonly used solvent has been methanol, Andy recently generated a web service to predict solubility in that solvent.
By combining these two approaches, Andy has now created a modeling system that can not only generally predict solubility in a wide range (70+) of solvents - but it can also provide related data that can be used for modeling other phenomena such as intestinal absorption of a drug or crossing the blood-brain barrier.[Stovall 2007]
The idea is to use a Random Forest approach to select freely available descriptors to predict the Abraham descriptors for any solute. A separate service then generates predicted solubilities for a wide range of solvents based on these Abraham descriptors. I'm using the term "freely available" because - although the CDK descriptors and VCCLab services are open - the model requires 2 descriptors only available from ChemSpider (ultimately from ACD/Labs).
Here is an example with benzoic acid. As long as the common name resolves to a single entry on ChemSpider, it is enough to enter it and it automatically populates the rest of the fields, which are then used by the service to generate the Abraham descriptors.
Hitting the prediction link above will automatically populate the second service and generate predicted solubilities for over 70 solvents.
This approach of allowing people to access these components separately can be useful. It can be instructive to manually play with the Abraham descriptors directly to see how predicted solubilities are affected. There are also situations where one has experimentally determined Abraham descriptors for a solute and bypassing the descriptor prediction step is required.
However, for those who prefer to cut to the chase, a convenient web service is available where the common name (or SMILES) of the solute is entered and the list of available solvents appears as a drop down menu.
Now here is where I think the real payoff comes for accelerating science with openness. Andy has also created a web service that returns the predicted solubility in molar as a number from common names (or SMILES) for solute and solvent via the URL. For example click this for benzoic acid in methanol. The advantage here is that solubility prediction can be easily integrated as a web service call from intuitive interfaces such as a Google Spreadsheet to enable even non-programmers to make use of the data. Notice that the web service provided in the fourth column for the average of measured solubility values enables an easy way to explore the accuracy of specific predictions.
Such web services could also be integrated with data from ChemSpider or custom systems. If those who use these services feed back their processed data to the open web, it could take us a step closer to automated reaction design. For example consider the custom application to select solvents for the Ugi reaction. Model builders could also use the web services for predicted and measured solubility directly.
A while back we explored using Taverna for MyExperiment to create virtual libraries of SMILES. Unfortunately we ran into issues with getting the applications developed on Macs to run on our PCs. This might be worth revisiting as a means of filtering virtual libraries through different thresholds of predicted solubility.
Andy has described his model in detail in a fully transparent way - the model itself, how it was generated and the entire dataset can be found here. We would welcome improvements of the model as well as completely new models based on our dataset using only freely available tools.
It should be noted that when I use term "general" it refers to the ability for the model to generate a number for most compounds listed in ChemSpider. Obviously compounds that most closely resemble the training set are more likely to generate better estimates. Because of our synthetic objectives using the Ugi reaction we have mainly focused on collecting solubility data for carboxylic acids, aldehydes and amides either from new measurements or from the literature.
Another important point concerns the main intended application of the model: organic synthesis. Generally the range of interest for such applications is about 0.01 - 3M. This might be very different for other applications - such as the aqueous solubility of a drug, where distinctions between much lower solubilities may be important.
For a typical organic synthesis, a solubility of 0.001M or 0.005M will probably translate as effectively insoluble. This might be a desired property for a product intended to be isolated by filtration. On the other end of the scale knowing that a solubility is either 4M or 6M will not usually have an impact on reaction design. It is enough to know that a reactant will have good solubility in a particular solvent.
Given the above considerations for intended applications and the likelihood that the current model is far from optimized, the predictions should be used cautiously. We suggest that the model is best used as a "flagging device". For example, if a reaction is to be carried out at 0.5M, one may place a threshold at 0.4M for the predicted values of reactants during solvent selection, with the recognition that a predicted 0.4M may be an actual 0.55M. A similar threshold approach can be used for the product, where in this case the lowest solubility is desired. A practical example of this is the shortlisting of solvents candidates for the Ugi reaction.
Another example of flagging involves identifying the outliers in the model. These can be inspected for experimental errors and possibly remeasured. Alternatively outliers may shed light on the limitations of the model. For example we have found that the solubility of solutes with melting points near room temperature can be greatly underestimated by the current model. This may be an opportunity to develop other models which incorporate melting point or enthalpy of fusion.[Rohani 2008]
Although it is possible that better models and more data will improve the accuracy of the predictions, this can be true only if the training set is accurate enough. Based on conversations I've had with researchers who deal with solubility, reading modeling papers and our own experience with the ONS Challenge I am starting to suspect that much of the available data just isn't accurate enough for high precision modeling. Models using data from the literature are especially vulnerable I think. Take a look at this unsettling comparison between new measurements and literature values (not to mention the model) for common compounds.[Loftsson 2006] Here is a subset:I have also made the point in detail for the aqueous solubility of EGCG. Could this be the reason that so many different solubility models using different physical chemistry principles have evolved and continue to co-exist?
The situation reminds me a lot of the discussions taking place in the molecular docking community.[Bissantz 2010] The differences in calculated binding energies are often small in comparison with the uncertainties involved. But docking can still be used as one tool among others to find drug candidates by flagging a collection of compounds above a certain threshold binding energy.

A few days ago Andrew Lang suggested to Dustin Sprouse that he submit his thesis to the Reaction Attempts database. Like many undergraduates Dustin put in a lot of time and effort in doing experiments and writing up his results but didn't have quite enough time to obtain all that would have been required for a traditional publication.
A thesis is an unusual document within the context of scientific communication. Unlike a peer reviewed paper, it may contain a large number of "failed experiments" and a substantial amount of speculation. Although it is not quite as detailed as lab notebook, there is often plenty of raw data and details about how failed or ambiguous experiments proceeded.
In Dustin's case we felt that there was enough information provided to include his thesis in Reaction Attempts. In addition, his thesis was accepted by Nature Precedings, thus providing a convenient means of citation.
The first component of the Reaction Attempts project is to quickly abstract the most basic information from synthetic organic chemistry reactions. This includes the ChemSpiderIDs and SMILES from the reactants and target products and brief notes about conditions and outcomes. We are especially interested in failed or ambiguous experiments because these have almost no chance of being communicated and indexed in the traditional systems. When attempting to carry out a reaction, it can be just as useful to know what doesn't work - and more specifically how it doesn't work.
The second component of the project is dissemination. Because the information is encoded semantically, it can be automatically converted to both human and machine readable formats.
One human interface consists of a PDF book (also as a hard copy), with the option of selected reactions specified by listing CSIDs of reactants in the URL. For example Dustin's reactions can be presented selectively here. We also have a Reaction Explorer, where reactants or products can be selected from a dropdown menu or via a substructure search.

We also provide live XML feeds so that others can create applications easily from machine readable data. For example one could create reaction chains automatically, which will occur whenever we enter reactions from multi-step syntheses like Dustin's - based on the synthesis of resveratrol.
I know that Peter Murray-Rust has been very active in automatically abstracting information from chemistry theses. It would be interesting to see how that approach would work for this thesis, especially with the failed experiments. Reducing a page or two of text into only the most salient bits of information manually required a level of judgement that I imagine would be tricky to do automatically.

 Edge: A SLICE OF SCIFOO By Frank Wilczekwww.edge.orgPosted by kaythaney and 3 others to science foo camp scifoo on Tue Jul 20 2010 at 20:32 UTC | info | related

 Scifoo 2009 PhotosBEN LORICAThe Practical Quant, (14 Jul 2009)Posted by timo and 1 other to scifoo09 scifoo on Sun Oct 18 2009 at 12:41 UTC | info | related

Author Summary

Conducting clinical trials of new vaccines in rural, resource-limited areas can be challenging since the people living in these areas often have high levels of illiteracy, little experience with clinical research, and limited access to routine health care. Especially difficult is obtaining informed consent for participation in this type of research and ensuring that potential participants adequately understand the potential risks and benefits of participation. The researchers have been preparing a remote field site in the northeastern part of the state of Minas Gerais, Brazil, for clinical trials of experimental hookworm vaccines. A special educational video was designed based on the method of analogies to introduce new scientific concepts related to the researchers' work and to improve knowledge of hookworm, a disease that is highly prevalent in their community. A questionnaire was administered both before and after the video was shown to a group of adults at the field site, which demonstrated the effectiveness of the video in disseminating knowledge about hookworm infection and about the vaccine being developed. Therefore, even in a rural, resource-limited area, educational tools can be specially designed that significantly improve understanding and therefore the likelihood of obtaining truly informed consent for participation in clinical research.

Author Summary

For many years, we and others have used cysts of Entamoeba invadens (Ei), a reptilian parasite, to model the infectious and diagnostic cysts of the human pathogen Entamoeba histolytica (Eh). The Ei cyst wall is composed of chitin fibrils, as well as Jacob and Jessie lectins that have unique chitin-binding domains. Our recent results suggest a “wattle and daub” model of the Ei cyst wall, where the wattle or sticks (chitin fibrils bound by multivalent Jacob lectins) is constructed prior to the addition of the mortar or daub (self-aggregating Jessie3 lectins). Here we “humanize” the Ei model of the cyst wall with four findings. First, a recombinant Eh Jacob2 lectin, which has three predicted chitin-binding domains surrounding a large spacer domain, binds chitin beads. Second, polymorphisms in the spacer domain of EhJacob2 discriminate clinical isolates of Entamoeba. Third, chitinase, Jacob2 lectin, and Jessie3 lectin are present in cyst walls of clinical isolates of Entamoeba. Finally, numerous sera from patients infected with Entamoeba recognize recombinant Eh Jacob1 and Jessie3 lectins.

Author Summary

Mycobacterium ulcerans causes a destructive skin disease known as Buruli ulcer (BU), which has been reported from more than 30 tropical or subtropical countries, with the highest prevalence in Western Africa. Due to the striking genetic monomorphism of African M. ulcerans populations, conventional genetic fingerprinting methods have largely failed to differentiate isolates coming from the same BU endemic area. Here we report a highly discriminatory fingerprinting method for M. ulcerans using a single nucleotide polymorphism-based genetic fine-typing technique. This method has enabled us for the first time to identify different M. ulcerans haplotypes within a BU endemic area. Linking the origins of M. ulcerans strains with the patients' residences unveiled the clustering of unique M. ulcerans haplotypes within the Densu river basin of Ghana. Results show, that haplotypes do not spread within a short time over the entire BU endemic region, but rather form independent focal transmission clusters.

Author Summary

Scrub typhus, the rickettsial infectious disease caused by the obligate intracellular bacterium Orientia tsutsugamushi, is endemic across the Asia Pacific region. The bacterium is transmitted by the bite of larval stages of trombiculid mites (“chiggers”; Leptotrombidium spp.), which more typically feed on small rodents. Clinical features include fever, headache, myalgia, lymphadenopathy and an eschar at the site of the bite. Despite the importance of this pathogen, little is known of the population diversity or the role of homologous recombination in driving the microevolution of this species. Here, we describe the development and application of a multilocus sequence typing (MLST) scheme that can be applied directly to blood samples, and that was applied to 108 O. tsutsugamushi isolates. We found that this organism demonstrated a high rate of homologous recombination, a surprising finding given the intracellular life-style of this species. We also found that 25% of patients in our study were simultaneously infected with multiple sequence types, suggesting multiple infection caused by either multiple mite bites, or multiple strains co-existing within individual mites.