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991.
Amit Sharma Alison Slaughter Nivedita Jena Lei Feng Jacques J. Kessl Hind J. Fadel Nirav Malani Frances Male Li Wu Eric Poeschla Frederic D. Bushman James R. Fuchs Mamuka Kvaratskhelia 《PLoS pathogens》2014,10(5)
The quinoline-based allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are promising candidates for clinically useful antiviral agents. Studies using these compounds have highlighted the role of IN in both early and late stages of virus replication. However, dissecting the exact mechanism of action of the quinoline-based ALLINIs has been complicated by the multifunctional nature of these inhibitors because they both inhibit IN binding with its cofactor LEDGF/p75 and promote aberrant IN multimerization with similar potencies in vitro. Here we report design of small molecules that allowed us to probe the role of HIV-1 IN multimerization independently from IN-LEDGF/p75 interactions in infected cells. We altered the rigid quinoline moiety in ALLINIs and designed pyridine-based molecules with a rotatable single bond to allow these compounds to bridge between interacting IN subunits optimally and promote oligomerization. The most potent pyridine-based inhibitor, KF116, potently (EC50 of 0.024 µM) blocked HIV-1 replication by inducing aberrant IN multimerization in virus particles, whereas it was not effective when added to target cells. Furthermore, KF116 inhibited the HIV-1 IN variant with the A128T substitution, which confers resistance to the majority of quinoline-based ALLINIs. A genome-wide HIV-1 integration site analysis demonstrated that addition of KF116 to target or producer cells did not affect LEDGF/p75-dependent HIV-1 integration in host chromosomes, indicating that this compound is not detectably inhibiting IN-LEDGF/p75 binding. These findings delineate the significance of correctly ordered IN structure for HIV-1 particle morphogenesis and demonstrate feasibility of exploiting IN multimerization as a therapeutic target. Furthermore, pyridine-based compounds present a novel class of multimerization selective IN inhibitors as investigational probes for HIV-1 molecular biology. 相似文献
992.
Deok-Song Kim Myra Hosmillo Mia Madel Alfajaro Ji-Yun Kim Jun-Gyu Park Kyu-Yeol Son Eun-Hye Ryu Frederic Sorgeloos Hyung-Jun Kwon Su-Jin Park Woo Song Lee Duck Cho Joseph Kwon Jong-Soon Choi Mun-Il Kang Ian Goodfellow Kyoung-Oh Cho 《PLoS pathogens》2014,10(6)
Sapovirus, a member of the Caliciviridae family, is an important cause of acute gastroenteritis in humans and pigs. Currently, the porcine sapovirus (PSaV) Cowden strain remains the only cultivable member of the Sapovirus genus. While some caliciviruses are known to utilize carbohydrate receptors for entry and infection, a functional receptor for sapovirus is unknown. To characterize the functional receptor of the Cowden strain of PSaV, we undertook a comprehensive series of protein-ligand biochemical assays in mock and PSaV-infected cell culture and/or piglet intestinal tissue sections. PSaV revealed neither hemagglutination activity with red blood cells from any species nor binding activity to synthetic histo-blood group antigens, indicating that PSaV does not use histo-blood group antigens as receptors. Attachment and infection of PSaV were markedly blocked by sialic acid and Vibrio cholerae neuraminidase (NA), suggesting a role for α2,3-linked, α2,6-linked or α2,8-linked sialic acid in virus attachment. However, viral attachment and infection were only partially inhibited by treatment of cells with sialidase S (SS) or Maackia amurensis lectin (MAL), both specific for α2,3-linked sialic acid, or Sambucus nigra lectin (SNL), specific for α2,6-linked sialic acid. These results indicated that PSaV recognizes both α2,3- and α2,6-linked sialic acids for viral attachment and infection. Treatment of cells with proteases or with benzyl 4-O-β-D-galactopyranosyl-β-D-glucopyranoside (benzylGalNAc), which inhibits O-linked glycosylation, also reduced virus binding and infection, whereas inhibition of glycolipd synthesis or N-linked glycosylation had no such effect on virus binding or infection. These data suggest PSaV binds to cellular receptors that consist of α2,3- and α2,6-linked sialic acids on glycoproteins attached via O-linked glycosylation. 相似文献
993.
Kyle Bittinger Emily S Charlson Elizabeth Loy David J Shirley Andrew R Haas Alice Laughlin Yanjie Yi Gary D Wu James D Lewis Ian Frank Edward Cantu Joshua M Diamond Jason D Christie Ronald G Collman Frederic D Bushman 《Genome biology》2014,15(10)
Background
Fungi are important pathogens but challenging to enumerate using next-generation sequencing because of low absolute abundance in many samples and high levels of fungal DNA from contaminating sources.Results
Here, we analyze fungal lineages present in the human airway using an improved method for contamination filtering. We use DNA quantification data, which are routinely acquired during DNA library preparation, to annotate output sequence data, and improve the identification and filtering of contaminants. We compare fungal communities and bacterial communities from healthy subjects, HIV+ subjects, and lung transplant recipients, providing a gradient of increasing lung impairment for comparison. We use deep sequencing to characterize ribosomal rRNA gene segments from fungi and bacteria in DNA extracted from bronchiolar lavage samples and oropharyngeal wash. Comparison to clinical culture data documents improved detection after applying the filtering procedure.Conclusions
We find increased representation of medically relevant organisms, including Candida, Cryptococcus, and Aspergillus, in subjects with increasingly severe pulmonary and immunologic deficits. We analyze covariation of fungal and bacterial taxa, and find that oropharyngeal communities rich in Candida are also rich in mitis group Streptococci, a community pattern associated with pathogenic polymicrobial biofilms. Thus, using this approach, it is possible to characterize fungal communities in the human respiratory tract more accurately and explore their interactions with bacterial communities in health and disease.Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0487-y) contains supplementary material, which is available to authorized users. 相似文献994.
Thomas Vanhercke Anna El Tahchy Qing Liu Xue‐Rong Zhou Pushkar Shrestha Uday K. Divi Jean‐Philippe Ral Maged P. Mansour Peter D. Nichols Christopher N. James Patrick J. Horn Kent D. Chapman Frederic Beaudoin Noemi Ruiz‐López Philip J. Larkin Robert C. de Feyter Surinder P. Singh James R. Petrie 《Plant biotechnology journal》2014,12(2):231-239
High biomass crops have recently attracted significant attention as an alternative platform for the renewable production of high energy storage lipids such as triacylglycerol (TAG). While TAG typically accumulates in seeds as storage compounds fuelling subsequent germination, levels in vegetative tissues are generally low. Here, we report the accumulation of more than 15% TAG (17.7% total lipids) by dry weight in Nicotiana tabacum (tobacco) leaves by the co‐expression of three genes involved in different aspects of TAG production without severely impacting plant development. These yields far exceed the levels found in wild‐type leaf tissue as well as previously reported engineered TAG yields in vegetative tissues of Arabidopsis thaliana and N. tabacum. When translated to a high biomass crop, the current levels would translate to an oil yield per hectare that exceeds those of most cultivated oilseed crops. Confocal fluorescence microscopy and mass spectrometry imaging confirmed the accumulation of TAG within leaf mesophyll cells. In addition, we explored the applicability of several existing oil‐processing methods using fresh leaf tissue. Our results demonstrate the technical feasibility of a vegetative plant oil production platform and provide for a step change in the bioenergy landscape, opening new prospects for sustainable food, high energy forage, biofuel and biomaterial applications. 相似文献
995.
Identity-by-descent probabilities are important for many applications in genetics. Here we propose a method for modeling the transmission of the haplotypes from the closest genotyped relatives along an entire chromosome. The method relies on a hidden Markov model where hidden states correspond to the set of all possible origins of a haplotype within a given pedigree. Initial state probabilities are estimated from average genetic contribution of each origin to the modeled haplotype while transition probabilities are computed from recombination probabilities and pedigree relationships between the modeled haplotype and the various possible origins. The method was tested on three simulated scenarios based on real data sets from dairy cattle, Arabidopsis thaliana, and maize. The mean identity-by-descent probabilities estimated for the truly inherited parental chromosome ranged from 0.94 to 0.98 according to the design and the marker density. The lowest values were observed in regions close to crossing over or where the method was not able to discriminate between several origins due to their similarity. It is shown that the estimated probabilities were correctly calibrated. For marker imputation (or QTL allele prediction for fine mapping or genomic selection), the method was efficient, with 3.75% allelic imputation error rates on a dairy cattle data set with a low marker density map (1 SNP/Mb). The method should prove useful for situations we are facing now in experimental designs and in plant and animal breeding, where founders are genotyped with relatively high markers densities and last generation(s) genotyped with a lower-density panel. 相似文献
996.
de Medina P Paillasse MR Ségala G Khallouki F Brillouet S Dalenc F Courbon F Record M Poirot M Silvente-Poirot S 《Chemistry and physics of lipids》2011,(6):432-437
Tamoxifen is one of the major drugs used for the hormonotherapy of estrogen receptor positive breast cancers. However, its therapeutic efficacy can be limited by acquired resistance and tumor recurrence can occur after several years of treatment. Tamoxifen is known as the prototypical modulator of estrogen receptors, but other targets have been identified that could account for its pharmacology. In particular, tamoxifen binds with high affinity to the microsomal antiestrogen binding site (AEBS) and inhibits cholesterol esterification at therapeutic doses. We have recently shown that the AEBS was a hetero-oligomeric complex composed of 3β-hydroxysterol-Δ(8)-Δ(7)-isomerase and 3β-hydroxysterol-Δ(7)-reductase, that binds different structural classes of ligands, including selective estrogen receptor modulators, several sigma receptor ligands, poly-unsaturated fatty acids and ring B oxysterols. We established a link between the modulation of cholesterol metabolism by tamoxifen and other AEBS ligands and their capacity to induce breast cancer cell differentiation, apoptosis and autophagy. Moreover, we showed that the AEBS carries out cholesterol-5,6-epoxide hydrolase activity and established that cholesterol-5,6-epoxide hydrolase is a new target for tamoxifen and other AEBS ligands. Finally in this review, we report on recent data from the literature showing how the modulation of cholesterol and oxysterol metabolism can be linked to the antitumor and chemopreventive properties of tamoxifen, and give new perspectives to improve the clinical outcome of the hormonotherapy of breast cancers. 相似文献
997.
Akhmetzhanov AR Grognard F Mailleret L 《Evolution; international journal of organic evolution》2011,65(11):3113-3125
The interplay between individual adaptive life histories and populations dynamics is an important issue in ecology. In this context, we considered a seasonal consumer-resource model with nonoverlapping generations. We focused on the consumers decision-making process through which they maximize their reproductive output via a differential investment into foraging for resources or reproducing. Our model takes a semi-discrete form, and is composed of a continuous time within-season part, similar to a dynamic model of energy allocation, and of a discrete time part, depicting the between seasons reproduction and mortality processes. We showed that the optimal foraging-reproduction strategies of the consumers may be "determinate" or "indeterminate" depending on the season length. More surprisingly, it depended on the consumers population density as well, with large densities promoting indeterminacy. A bifurcation analysis showed that the long-term dynamics produced by this model were quite rich, ranging from both populations' extinction, coexistence at some season-to-season equilibrium or on (quasi)-periodic motions, to initial condition-dependent dynamics. Interestingly, we observed that any long-term sustainable situation corresponds to indeterminate consumers' strategies. Finally, a comparison with a model involving typical nonoptimal consumers highlighted the stabilizing effects of the optimal life histories of the consumers. 相似文献
998.
Navarro-Sastre A Tort F Stehling O Uzarska MA Arranz JA Del Toro M Labayru MT Landa J Font A Garcia-Villoria J Merinero B Ugarte M Gutierrez-Solana LG Campistol J Garcia-Cazorla A Vaquerizo J Riudor E Briones P Elpeleg O Ribes A Lill R 《American journal of human genetics》2011,(5):656-667
We report on ten individuals with a fatal infantile encephalopathy and/or pulmonary hypertension, leading to death before the age of 15 months. Hyperglycinemia and lactic acidosis were common findings. Glycine cleavage system and pyruvate dehydrogenase complex (PDHC) activities were low. Homozygosity mapping revealed a perfectly overlapping homozygous region of 1.24 Mb corresponding to chromosome 2 and led to the identification of a homozygous missense mutation (c.622G > T) in NFU1, which encodes a conserved protein suggested to participate in Fe-S cluster biogenesis. Nine individuals were homozygous for this mutation, whereas one was compound heterozygous for this and a splice-site (c.545 + 5G > A) mutation. The biochemical phenotype suggested an impaired activity of the Fe-S enzyme lipoic acid synthase (LAS). Direct measurement of protein-bound lipoic acid in individual tissues indeed showed marked decreases. Upon depletion of NFU1 by RNA interference in human cell culture, LAS and, in turn, PDHC activities were largely diminished. In addition, the amount of succinate dehydrogenase, but no other Fe-S proteins, was decreased. In contrast, depletion of the general Fe-S scaffold protein ISCU severely affected assembly of all tested Fe-S proteins, suggesting that NFU1 performs a specific function in mitochondrial Fe-S cluster maturation. Similar biochemical effects were observed in Saccharomyces cerevisiae upon deletion of NFU1, resulting in lower lipoylation and SDH activity. Importantly, yeast Nfu1 protein carrying the individuals' missense mutation was functionally impaired. We conclude that NFU1 functions as a late-acting maturation factor for a subset of mitochondrial Fe-S proteins. 相似文献
999.
1000.
Rodrigo Gonzalez-Valencia Armando Sepulveda-Jauregui Karla Martinez-Cruz Jorge Hoyos-Santillan Luc Dendooven Frederic Thalasso 《Hydrobiologia》2014,721(1):9-22
The literature concerning methane (CH4) emissions from temperate and boreal lakes is extensive, but emissions from tropical and subtropical lakes have been less documented. In particular, methane emissions from Mexican lakes, which are often polluted by anthropogenic carbon and nutrient inputs, have not been reported previously. In this work, methane emissions from six Mexican lakes were measured, covering a broad range of organic inputs, trophic states, and climatic conditions. Methane emissions ranged from 5 to 5,000 mg CH4 m?2 day?1. Water samples from several depths in each lake were analyzed for correlation between water quality indicators and methane emissions. Trophic state and water quality indexes were most strongly correlated with methane fluxes. The global methane flux from Mexican freshwater lakes was estimated to be approximately 1.3 Tg CH4 year?1, which is about 20% of methane and 4.4% of total national greenhouse gas emissions. Data for untreated wastewater releases to the environment gave an emission factor of 0.19 kg CH4 kg?1 of Biochemical Oxygen Demand, which is superior to that previously estimated by the IPCC for lake discharges. Thus, the large volume of untreated wastewater in Mexico implies higher methane emission than previously estimated. 相似文献