Nanopore sequencing and assembly of a human genome with ultra-long reads

Jain, M.; Koren, S.; Miga, K.H.; Quick, J.; Rand, A.C.; Sasani, T.A.; Tyson, J.R.; Beggs, A.D.; Dilthey, A.T.; Fiddes, I.T.; Malla, S.; Marriott, H.; Nieto, T.; O'Grady, J.; Olsen, H.E.; Pedersen, B.S.; Rhie, A.; Richardson, H.; Quinlan, A.R.; Snutch, T.P.; Tee, L.; Paten, B.; Phillippy, A.M.; Simpson, J.T.; Loman, N.J.; Loose, M.

doi:10.1038/nbt.4060

Understanding hepatitis C intervention success: qualitative findings from the HepCATT study (2018)
Journal Article
Harris, M., Bonnington, O., Harrison, G., Hickman, M., & Irving, W. L. (in press). Understanding hepatitis C intervention success: qualitative findings from the HepCATT study. Journal of Viral Hepatitis, https://doi.org/10.1111/jvh.12869

The United Kingdom has committed to eliminating viral hepatitis as a public health threat. Innovative interventions for marginalized populations are required to realize this goal. In 2016, the HepCATT study team implemented a complex hepatitis C (HCV... Read More about Understanding hepatitis C intervention success: qualitative findings from the HepCATT study.

Micro-pharmacokinetics: quantifying local drug concentration at live cell membranes (2018)
Journal Article
Gherbi, K., Briddon, S. J., & Charlton, S. J. (in press). Micro-pharmacokinetics: quantifying local drug concentration at live cell membranes. Scientific Reports, 8, Article 3479. https://doi.org/10.1038/s41598-018-21100-x

Fundamental equations for determining pharmacological parameters, such as the binding afnity of a ligand for its target receptor, assume a homogeneous distribution of ligand, with concentrations in the immediate vicinity of the receptor being the sam... Read More about Micro-pharmacokinetics: quantifying local drug concentration at live cell membranes.

Physiological, but not fitness, effects of two interacting haemoparasitic infections in a wild rodent (2018)
Journal Article
Taylor, C. H., Wanelik, K. M., Friberg, I. M., Lowe, A., Hall, A. J., Ralli, C., …Bradley, J. E. (2018). Physiological, but not fitness, effects of two interacting haemoparasitic infections in a wild rodent. International Journal for Parasitology, 48(6), 463-471. https://doi.org/10.1016/j.ijpara.2017.11.006

In contrast to the conditions in most laboratory studies, wild animals are routinely challenged by multiple infections at once, and these infections can interact in complex ways. This means that the impact of a parasite on its host’s physiology and f... Read More about Physiological, but not fitness, effects of two interacting haemoparasitic infections in a wild rodent.

Prophylactic antibiotic use in COPD and the potential anti-inflammatory activities of antibiotics (2018)
Journal Article
Huckle, A. W., Fairclough, L. C., & Todd, I. (2018). Prophylactic antibiotic use in COPD and the potential anti-inflammatory activities of antibiotics. Current Respiratory Care Reports, 63(5), https://doi.org/10.4187/respcare.05943

Antibiotics have previously demonstrated anti-inflammatory properties, and they have been linked to therapeutic benefit in several pulmonary conditions that feature inflammation. Previous research suggests that these anti-inflammatory properties may... Read More about Prophylactic antibiotic use in COPD and the potential anti-inflammatory activities of antibiotics.

Human dendritic cell sequestration onto the Necator americanus larval sheath during ex-sheathing: a possible mechanism for immune privilege (2018)
Journal Article
Hassan, A., Pritchard, D. I., & Ghaemmaghami, A. M. (2018). Human dendritic cell sequestration onto the Necator americanus larval sheath during ex-sheathing: a possible mechanism for immune privilege. Parasitology, 145(9), 1183-1190. https://doi.org/10.1017/S0031182018000136

Despite the profound health implications of Necator americanus (N. americanus) infection in humans, many aspects of its interaction with the host immune system are poorly understood. Here we investigated the early events at the interface of N. americ... Read More about Human dendritic cell sequestration onto the Necator americanus larval sheath during ex-sheathing: a possible mechanism for immune privilege.

Sarcopenic obesity and overall mortality: Results from the application of novel models of body composition phenotypes to the National Health and Nutrition Examination Survey 1999–2004 (2018)
Journal Article
Van Aller, C., Lara, J., C.M. Stephan, B., Donini, L. M., Heymsfield, S., Katzmarzyk, P. T., …Siervo, M. (2019). Sarcopenic obesity and overall mortality: Results from the application of novel models of body composition phenotypes to the National Health and Nutrition Examination Survey 1999–2004. Clinical Nutrition, 38(1), 264-270. https://doi.org/10.1016/j.clnu.2018.01.022

Background/Objectives There is no consensus on the definition of sarcopenic obesity (SO), resulting in inconsistent associations of SO with mortality risk. We aim to evaluate association of dual energy x-ray absorptiometry (DXA) SO models with mor... Read More about Sarcopenic obesity and overall mortality: Results from the application of novel models of body composition phenotypes to the National Health and Nutrition Examination Survey 1999–2004.

Maximal-intensity exercise does not fully restore muscle pyruvate dehydrogenase complex activation after 3 days of high-fat dietary intake (2018)
Journal Article
Constantin-Teodosiu, D., Cederblad, G., Bergstrom, M., & Greenhaff, P. L. (2019). Maximal-intensity exercise does not fully restore muscle pyruvate dehydrogenase complex activation after 3 days of high-fat dietary intake. Clinical Nutrition, 38(2), 948-953. https://doi.org/10.1016/j.clnu.2018.02.001

© 2019 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism Background & aims: Exercise activates muscle pyruvate dehydrogenase complex (PDC), but moderate intensity exercise fails to fully activate muscle PDC after high-fat diet [... Read More about Maximal-intensity exercise does not fully restore muscle pyruvate dehydrogenase complex activation after 3 days of high-fat dietary intake.

Postoperative inflammation and insulin resistance in relation to body composition, adiposity and carbohydrate treatment: a randomised controlled study (2018)
Journal Article
Tewari, N., Awad, S., Duška, F., Williams, J. P., Bennett, A., MacDonald, I. A., & Lobo, D. N. (2018). Postoperative inflammation and insulin resistance in relation to body composition, adiposity and carbohydrate treatment: a randomised controlled study. Clinical Nutrition, https://doi.org/10.1016/j.clnu.2018.01.032

Background and Aims: The aims of this study were to identify whether differences in distribution of adipose tissue and skeletal muscle in obese and non-obese individuals contribute to the magnitude of the postoperative inflammatory response and insul... Read More about Postoperative inflammation and insulin resistance in relation to body composition, adiposity and carbohydrate treatment: a randomised controlled study.

Elevation patterns of plant diversity and recent altitudinal range shifts in Sinai’s high mountain flora (2018)
Journal Article
Coals, P., Shmida, A., Vasl, A., Mansour, N., & Gilbert, F. (in press). Elevation patterns of plant diversity and recent altitudinal range shifts in Sinai’s high mountain flora. Journal of Vegetation Science, 29(2), https://doi.org/10.1111/jvs.12618

Questions: Is there evidence of recent altitudinal range shifts in a hyper-arid Middle Eastern desert mountain flora? How do the directions of shift for upper and lower altitudinal range limits of plants vary? Location: Hyper-arid mountain desert,... Read More about Elevation patterns of plant diversity and recent altitudinal range shifts in Sinai’s high mountain flora.

Characterization of behavioral, signaling and cytokine alterations in a rat neurodevelopmental model for schizophrenia, and their reversal by the 5-HT6 receptor antagonist SB-399885 (2018)
Journal Article

Post-weaning social isolation of rats produces neuroanatomical, neurochemical and behavioral alterations resembling some core features of schizophrenia. This study examined the ability of the 5-HT? receptor antagonist SB-399885 to reverse isolation-i... Read More about Characterization of behavioral, signaling and cytokine alterations in a rat neurodevelopmental model for schizophrenia, and their reversal by the 5-HT6 receptor antagonist SB-399885.

Integrin-β4 is a novel transcriptional target of TAp73 (2018)
Journal Article
Xie, N., Vikhreva, P., Annicchiarico-Petruzzelli, M., Amelio, I., Barlev, N., Knight, R. A., & Melino, G. (2018). Integrin-β4 is a novel transcriptional target of TAp73. Cell Cycle, 17(5), 589-594. https://doi.org/10.1080/15384101.2017.1403684

As a member of p53 family, p73 has attracted intense investigations due to its structural and functional similarities to p53. Among more than ten p73 variants, the transactivation (TA) domain-containing isoform TAp73 is the one that imitates the p53'... Read More about Integrin-β4 is a novel transcriptional target of TAp73.

A candidate tolerance gene identified in a natural population of field voles (Microtus agrestis) (2018)
Journal Article
Wanelik, K. M., Begon, M., Birtles, R. J., Bradley, J. E., Friberg, I. M., Jackson, J. A., …Paterson, S. (in press). A candidate tolerance gene identified in a natural population of field voles (Microtus agrestis). Molecular Ecology, 27(4), https://doi.org/10.1111/mec.14476

The animal immune response has hitherto been viewed primarily in the context of resistance only. However, individuals can also employ a tolerance strategy to maintain good health in the face of ongoing infection. To shed light on the genetic and phys... Read More about A candidate tolerance gene identified in a natural population of field voles (Microtus agrestis).

Heterologous expression of a novel drug transporter from the malaria parasite alters resistance to quinoline antimalarials (2018)
Journal Article
Tindall, S. M., Vallières, C., Lakhani, D. H., Islahudin, F., Ting, K.-N., & Avery, S. V. (in press). Heterologous expression of a novel drug transporter from the malaria parasite alters resistance to quinoline antimalarials. Scientific Reports, 8(1), https://doi.org/10.1038/s41598-018-20816-0

Antimalarial drug resistance hampers effective malaria treatment. Critical SNPs in a particular, putative amino acid transporter were recently linked to chloroquine (CQ) resistance in malaria parasites. Here, we show that this conserved protein (PF3D... Read More about Heterologous expression of a novel drug transporter from the malaria parasite alters resistance to quinoline antimalarials.

To boil an egg: substrate binding affects critical stability in thermal unfolding of proteins (2018)
Journal Article
Hussain, R., Hughes, C. S., Jávorfi, T., Siligardi, G., Williams, P., & Bonev, B. B. (2018). To boil an egg: substrate binding affects critical stability in thermal unfolding of proteins. Journal of Physical Chemistry B, 122(8), 2213-2218. https://doi.org/10.1021/acs.jpcb.7b10643

Thermal unfolding of proteins is used extensively in screening of drug candidates because molecular interactions with ligands and substrates affect strongly protein stability, transition temperature, and cooperativity. We use synchrotron radiation ci... Read More about To boil an egg: substrate binding affects critical stability in thermal unfolding of proteins.

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas (2018)
Journal Article
Humphreys, C. M., & Minton, N. P. (in press). Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas. Current Opinion in Biotechnology, 50, https://doi.org/10.1016/j.copbio.2017.12.023

The future sustainable production of chemicals and fuels from non-petrochemical sources, while at the same time reducing greenhouse gas (GHG) emissions, represent two of society's greatest challenges. Microbial chassis able to grow on waste carbon mo... Read More about Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas.

Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: a systematic review (2018)
Journal Article
Walker, A. J., Peacock, C. J., Pedergnana, V., & Irving, W. L. (in press). Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: a systematic review. Journal of Viral Hepatitis, 25(5), https://doi.org/10.1111/jvh.12871

Hepatitis C virus (HCV)-infected patients are at risk of developing hepatocellular carcinoma (HCC). Individuals at heightened riskcould be targeted by intensive follow-up surveillance. We have conducted a systematic review of the literature to identi... Read More about Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: a systematic review.

Mendelian adult-onset leukodystrophy genes in Alzheimer´s disease. Critical influence of CSF1R and NOTCH3 (2018)
Journal Article
Sassi, C., Nalls, M., Ridge, P., Gibbs, R., Lupton, M., Troakes, C., …Hardy, J. (in press). Mendelian adult-onset leukodystrophy genes in Alzheimer´s disease. Critical influence of CSF1R and NOTCH3. Neurobiology of Aging, 66, Article 179.e17-179.e29. https://doi.org/10.1016/j.neurobiolaging.2018.01.015

Mendelian adult-onset leukodystrophies are a spectrum of rare inherited progressive neurodegenerative disorders affecting the white matter of the central nervous system. Among these, Cerebral Autosomal Dominant and Recessive Arteriopathy with Subcort... Read More about Mendelian adult-onset leukodystrophy genes in Alzheimer´s disease. Critical influence of CSF1R and NOTCH3.

Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake (2018)
Journal Article
Dalwadi, M. P., Wang, Y., King, J. R., & Minton, N. P. (2018). Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake. SIAM Journal on Applied Mathematics, 78(3), 1300-1329. https://doi.org/10.1137/17m1138625

In mathematical models that include nutrient delivery to bacteria, it is prohibitively expensive to include a pointwise nutrient uptake within small bacterial regions over bioreactor length-scales, and so such models often impose an effective uptake... Read More about Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake.

Large Scale In Vivo Recording of Sensory Neuron Activity with GCaMP6 (2018)
Journal Article
Chisholm, K., Khovanov, N., Lopes, D. M., La Russa, F., & McMahon, S. B. (2018). Large Scale In Vivo Recording of Sensory Neuron Activity with GCaMP6. eNeuro, 5(1), Article ENEURO.0417-17.2018. https://doi.org/10.1523/eneuro.0417-17.2018

Greater emphasis on the study of intact cellular networks in their physiological environment has led to rapid advances in intravital imaging of the central nervous system (CNS), while the peripheral system remains largely unexplored. To assess large... Read More about Large Scale In Vivo Recording of Sensory Neuron Activity with GCaMP6.

Nanopore sequencing and assembly of a human genome with ultra-long reads (2018)
Journal Article
Jain, M., Koren, S., Miga, K., Quick, J., Rand, A., Sasani, T., …Loose, M. (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology, 36(4), 338-345. https://doi.org/10.1038/nbt.4060

© 2018 Nature Publishing Group. All rights reserved. We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, r... Read More about Nanopore sequencing and assembly of a human genome with ultra-long reads.

All Outputs (177)