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Find video protocols related to scientific articles indexed in Pubmed.
Structural studies provide clues for analog design of specific inhibitors of Cryptosporidium hominis thymidylate synthase-dihydrofolate reductase.
Bioorg. Med. Chem. Lett.
PUBLISHED: 07-24-2014
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Cryptosporidium is the causative agent of a gastrointestinal disease, cryptosporidiosis, which is often fatal in immunocompromised individuals and children. Thymidylate synthase (TS) and dihydrofolate reductase (DHFR) are essential enzymes in the folate biosynthesis pathway and are well established as drug targets in cancer, bacterial infections, and malaria. Cryptosporidium hominis has a bifunctional thymidylate synthase and dihydrofolate reductase enzyme, compared to separate enzymes in the host. We evaluated lead compound 1 from a novel series of antifolates, 2-amino-4-oxo-5-substituted pyrrolo[2,3-d]pyrimidines as an inhibitor of Cryptosporidium hominis thymidylate synthase with selectivity over the human enzyme. Complementing the enzyme inhibition compound 1 also has anti-cryptosporidial activity in cell culture. A crystal structure with compound 1 bound to the TS active site is discussed in terms of several van der Waals, hydrophobic and hydrogen bond interactions with the protein residues and the substrate analog 5-fluorodeoxyuridine monophosphate (TS), cofactor NADPH and inhibitor methotrexate (DHFR). Another crystal structure in complex with compound 1 bound in both the TS and DHFR active sites is also reported here. The crystal structures provide clues for analog design and for the design of ChTS-DHFR specific inhibitors.
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Engineering the structure of an N-terminal ?-turn to maximize screw-sense preference in achiral helical peptide chains.
J. Org. Chem.
PUBLISHED: 04-24-2014
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Oligomers of ?-aminoisobutyric acid (Aib) are achiral peptides that typically adopt 310 helical conformations in which enantiomeric left- and right-handed conformers are, necessarily, equally populated. Incorporating a single protected chiral residue at the N-terminus of the peptide leads to induction of a screw-sense preference in the helical chain, which may be quantified (in the form of "helical excess") by NMR spectroscopy. Variation of this residue and its N-terminal protecting group leads to the conclusion that maximal levels of screw-sense preference are induced by bulky chiral tertiary amino acids carrying amide protecting groups or by chiral quaternary amino acids carrying carbamate protecting groups. Tertiary L-amino acids at the N-terminus of the oligomer induce a left-handed screw sense, while quaternary L-amino acids induce a right-handed screw sense. A screw-sense preference may also be induced from the second position of the chain, weakly by tertiary amino acids, and much more powerfully by quaternary amino acids. In this position, the L enantiomers of both families induce a right-handed screw sense. Maximal, and essentially quantitative, control is induced by an L-?-methylvaline residue at both positions 1 and 2 of the chain, carrying an N-terminal carbamate protecting group.
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Bayesian inference of epidemics on networks via belief propagation.
Phys. Rev. Lett.
PUBLISHED: 03-17-2014
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We study several Bayesian inference problems for irreversible stochastic epidemic models on networks from a statistical physics viewpoint. We derive equations which allow us to accurately compute the posterior distribution of the time evolution of the state of each node given some observations. At difference with most existing methods, we allow very general observation models, including unobserved nodes, state observations made at different or unknown times, and observations of infection times, possibly mixed together. Our method, which is based on the belief propagation algorithm, is efficient, naturally distributed, and exact on trees. As a particular case, we consider the problem of finding the "zero patient" of a susceptible-infected-recovered or susceptible-infected epidemic given a snapshot of the state of the network at a later unknown time. Numerical simulations show that our method outperforms previous ones on both synthetic and real networks, often by a very large margin.
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Nucleic acid test to diagnose cryptosporidiosis: lab assessment in animal and patient specimens.
Anal. Chem.
PUBLISHED: 02-12-2014
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Diarrheal diseases cause more morbidity and mortality around the world than human immunodeficiency virus (HIV), malaria, or tuberculosis. Given that effective treatment of persistent diarrheal illness requires knowledge of the causative organism, diagnostic tests are of paramount importance. The protozoan parasites of the genus Cryptosporidium are increasingly recognized to be responsible for a significant portion of diarrhea morbidity. We present a novel nucleic acid test to detect the presence of Cryptosporidium species in DNA extracted from stool samples. The assay uses the isothermal amplification technique recombinase polymerase amplification (RPA) to amplify trace amounts of pathogen DNA extracted from stool to detectable levels in 30 min; products are then detected visually on simple lateral flow strips. The RPA-based Cryptosporidium assay (RPAC assay) was developed and optimized using DNA from human stool samples spiked with pathogen. It was then tested using DNA extracted from the stool of infected mice where it correctly identified the presence or absence of 27 out of 28 stool samples. It was finally tested using DNA extracted from the stool of infected patients where it correctly identified the presence or absence of 21 out of 21 stool samples. The assay was integrated into a foldable, paper and plastic device that enables DNA amplification with only the use of pipets, pipet tips, and a heater. The performance of the integrated assay is comparable to or better than polymerase chain reaction (PCR), without requiring the use of thermal cycling equipment. This platform can easily be adapted to detect DNA from multiple pathogens.
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A novel calcium-dependent protein kinase inhibitor as a lead compound for treating cryptosporidiosis.
J. Infect. Dis.
PUBLISHED: 07-21-2013
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Cryptosporidium parasites infect intestinal cells, causing cryptosporidiosis. Despite its high morbidity and association with stunting in the developing world, current therapies for cryptosporidiosis have limited efficacy. Calcium-dependent protein kinases (CDPKs) are essential enzymes in the biology of protozoan parasites. CDPK1 was cloned from the genome of Cryptosporidium parvum, and potent and specific inhibitors have been developed based on structural studies. In this study, we evaluated the anti-Cryptosporidium activity of a novel CDPK1 inhibitor, 1294, and demonstrated that 1294 significantly reduces parasite infection in vitro, with a half maximal effective concentration of 100 nM. Pharmacokinetic studies revealed that 1294 is well absorbed, with a half-life supporting daily administration. Oral therapy with 1294 eliminated Cryptosporidium parasites from 6 of 7 infected severe combined immunodeficiency-beige mice, and the parasites did not recur in these immunosuppressed mice. Mice treated with 1294 had less epithelial damage, corresponding to less apoptosis. Thus, 1294 is an important lead for the development of drugs for treatment of cryptosporidiosis.
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Human primary intestinal epithelial cells as an improved in vitro model for Cryptosporidium parvum infection.
Infect. Immun.
PUBLISHED: 03-18-2013
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The study of human intestinal pathogens has been limited by the lack of methods for the long-term culture of primary human intestinal epithelial cells (PECs). The development of infection models with PECs would allow a better understanding of host-parasite interactions. The objective of this study was to develop a novel method for prolonged in vitro cultivation of PECs that can be used to study Cryptosporidium infection. We isolated intact crypts from human intestines removed during weight loss surgery. The fragments of intestinal layers were cultivated with culture medium supplemented with growth factors and antiapoptotic molecules. After 7 days, the PECs formed self-regenerating cell clusters, forming villi that resemble intestinal epithelium. The PECs proliferated and remained viable for at least 60 days. The cells expressed markers for intestinal stem cells, epithelial cells, and mature enterocytes. The PECs were infected with Cryptosporidium. In contrast to older models in which parasite numbers decay, the burden of parasites increased for >120 h. In summary, we describe here a novel method for the cultivation of self-regenerating human epithelial cells from small intestinal crypts, which contain both intestinal stem cells and mature villus cells. We present data that suggest these cells support Cryptosporidium better than existing cell lines. PECs should provide an improved tool for studying host-parasite interactions involving Cryptosporidium and other intestinal pathogens.
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Current methods for asymmetric halogenation of olefins.
Chemistry
PUBLISHED: 04-20-2011
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This Minireview discusses the progress made in developing reactions where an olefin is subjected to an asymmetric halogenation. It aims to serve as a reference for the studies reported to date, including preliminary work and mechanistic studies. The current state of the art, scope, and limitations of these processes are discussed.
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Inference algorithm for finite-dimensional spin glasses: belief propagation on the dual lattice.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 02-18-2011
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Starting from a cluster variational method, and inspired by the correctness of the paramagnetic ansatz [at high temperatures in general, and at any temperature in the two-dimensional (2D) Edwards-Anderson (EA) model] we propose a message-passing algorithm--the dual algorithm--to estimate the marginal probabilities of spin glasses on finite-dimensional lattices. We use the EA models in 2D and 3D as benchmarks. The dual algorithm improves the Bethe approximation, and we show that in a wide range of temperatures (compared to the Bethe critical temperature) our algorithm compares very well with Monte Carlo simulations, with the double-loop algorithm, and with exact calculation of the ground state of 2D systems with bimodal and Gaussian interactions. Moreover, it is usually 100 times faster than other provably convergent methods, as the double-loop algorithm. In 2D and 3D the quality of the inference deteriorates only where the correlation length becomes very large, i.e., at low temperatures in 2D and close to the critical temperature in 3D.
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Immune responses and protection of Aotus monkeys immunized with irradiated Plasmodium vivax sporozoites.
Am. J. Trop. Med. Hyg.
PUBLISHED: 02-05-2011
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A non-human primate model for the induction of protective immunity against the pre-erythrocytic stages of Plasmodium vivax malaria using radiation-attenuated P. vivax sporozoites may help to characterize protective immune mechanisms and identify novel malaria vaccine candidates. Immune responses and protective efficacy induced by vaccination with irradiated P. vivax sporozoites were evaluated in malaria-naive Aotus monkeys. Three groups of six monkeys received two, five, or ten intravenous inoculations, respectively, of 100,000 irradiated P. vivax sporozoites; control groups received either 10 doses of uninfected salivary gland extract or no inoculations. Immunization resulted in the production low levels of antibodies that specifically recognized P. vivax sporozoites and the circumsporozoite protein. Additionally, immunization induced low levels of antigen-specific IFN-? responses. Intravenous challenge with viable sporozoites resulted in partial protection in a dose-dependent manner. These findings suggest that the Aotus monkey model may be able to play a role in preclinical development of P. vivax pre-erythrocytic stage vaccines.
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Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii.
ACS Med Chem Lett
PUBLISHED: 12-01-2010
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The protozoans Cryptosporidium parvum and Toxoplasma gondii are parasites of major health concern to humans. Both parasites contain a group of calcium-dependent protein kinases (CDPKs), which are found in plants and ciliates but not in humans or fungi. Here we describe a series of potent inhibitors that target CDPK1 in C. parvum (CpCDPK1) and T. gondii (TgCDPK1). These inhibitors are highly selective for CpCDPK1 and TgCDPK1 over the mammalian kinases SRC and ABL. Furthermore, they are able to block an early stage of C. parvum invasion of HCT-8 host cells, which is similar to their effects on T. gondii invasion of human fibroblasts.
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Human CD8(+) T cells clear Cryptosporidium parvum from infected intestinal epithelial cells.
Am. J. Trop. Med. Hyg.
PUBLISHED: 03-30-2010
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Intracellular protozoans of the genus Cryptosporidium are a major cause of diarrheal illness worldwide, especially in immunocompromised individuals. CD4(+) T cells and interferon-gamma are key factors in the control of cryptosporidiosis in human and murine models. Previous studies led us to hypothesize that CD8(+) T cells contribute to clearance of intestinal epithelial Cryptosporidium infection in humans. We report here that antigen expanded sensitized CD8(+) T cells reduce the parasite load in infected intestinal epithelial cell cultures and lyse infected intestinal epithelial cells. These effects are most likely mediated by the release of cytotoxic granules. Elimination of parasites seems to require antigen presentation through both human leukocyte antigen (HLA)-A and HLA-B. These data suggest that cytotoxic CD8(+) T cells play a role in clearing Cryptosporidium from the intestine, a previously unrecognized feature of the human immune response against this parasite.
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Oligonucleotide-gold nanoparticle networks for detection of Cryptosporidium parvum heat shock protein 70 mRNA.
J. Clin. Microbiol.
PUBLISHED: 10-14-2009
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We report on a novel strategy for the detection of mRNA targets derived from Cryptosporidium parvum oocysts by the use of oligonucleotide-gold nanoparticles. Gold nanoparticles are functionalized with oligonucleotides which are complementary to unique sequences present on the heat shock protein 70 (HSP70) DNA/RNA target. The results indicate that the presence of HPS70 targets of increasing complexity causes the formation of oligonucleotide-gold nanoparticle networks which can be visually monitored via a simple colorimetric readout measured by a total internal reflection imaging setup. Furthermore, the induced expression of HSP70 mRNA in Cryptosporidium parvum oocysts via a simple heat shock process provides nonenzymatic amplification such that the HSP70 mRNA derived from as few as 5 x 10(3) purified C. parvum oocysts was successfully detected. Taken together, these results support the use of oligonucleotide-gold nanoparticles for the molecular diagnosis of cryptosporidiosis, offering new opportunities for the further development of point-of-care diagnostic assays with low-cost, robust reagents and simple colorimetric detection.
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Highly diastereoselective Katsuki-Jacobsen oxidation-epoxidation of alpha-silyloxy sulfinyl dienes: synthetic applications.
J. Org. Chem.
PUBLISHED: 02-13-2009
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Katsuki-Jacobsen oxidation-epoxidation of acyclic alpha-silyloxy sulfinyl dienes, followed by acid-promoted cyclization, leads to 2,5-trans-sulfonyl dihydrofurans with good selectivities. As an application, the formal syntheses of (6S,7S,9R,10R)- and (6S,7S,9S,10S)-6,9-epoxynonadec-18-ene-7,10-diols is reported.
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Benzoylbenzimidazole-based selective inhibitors targeting Cryptosporidium parvum and Toxoplasma gondii calcium-dependent protein kinase-1.
Bioorg. Med. Chem. Lett.
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Calcium-dependent protein kinase-1 (CDPK1) from Cryptosporidium parvum (CpCDPK1) and Toxoplasma gondii (TgCDPK1) have become attractive targets for discovering selective inhibitors to combat infections caused by these protozoa. We used structure-based design to improve a series of benzoylbenzimidazole-based compounds in terms of solubility, selectivity, and potency against CpCDPK1 and TgCDPK1. The best inhibitors show inhibitory potencies below 50 nM and selectivity well above 200-fold over two human kinases with small gatekeeper residues.
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Treatable bacterial infections are underrecognized causes of fever in Ethiopian children.
Am. J. Trop. Med. Hyg.
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Febrile illnesses remain a major cause of morbidity and mortality in resource-poor countries, but too often, tests are not available to determine the causes, leading to misdiagnosis and inappropriate treatment. To determine the cause of febrile illnesses, we recovered the malaria smears from 102 children presenting with fever to Soddo Christian Hospital in Wolaitta Soddo, Ethiopia. DNA was isolated from the smears and evaluated by real-time polymerase chain reaction. We identified pathogen DNA with probes for Plasmodium spp., Streptococcus pneumoniae, Rickettsia spp., Salmonella spp., and Borrelia spp. Overall, we showed that it is possible to isolate high-quality DNA and identify treatable pathogens from malaria blood smears. Furthermore, our data showed that bacterial pathogens (especially Pneumococcus, Rickettsia spp., and Borrelia spp.) are common and frequently unrecognized but treatable causes of febrile illnesses in Ethiopian children.
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[Tension pneumoperitoneum as a complication of endoscopic ultrasound guided transgastric drainage of pancreatic pseudocyst: case report and review of the literature].
Rev Gastroenterol Peru
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Pancreatic pseudocyst develops as a complication in some cases of pancreatitis. Endoscopic drainage is one of the available therapies, but it has limitations when a visible compression over the gastric or duodenal wall is not present, or when portal hypertension exists. Endoscopic ultrasonography allows for a guided approach even in cases where external compression over the gastrointestinal tract is barely visible or non-existent, and it also helps to prevent vascular injury during puncture of the fluid collection. The most frequent early complications related to cystogastrostomy and cystoduodenostomy are bleeding and pneumoperitoneum, and late complications are stent migration or occlusion, and infection. We report the case of a patient who developed tense pneumoperitoneum immediately after endoscopic ultrasound guided drainage of a pancreatic pseudocyst, and was treated conservatively. This is a severe event, and can be managed by emergency decompression through paracentesis as first line therapy. Most cases of pneumoperitoneum can be managed without surgery,but close observation is mandatory in order to timely detect and treat conditions needing surgical intervention.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.