Structural basis of West Nile virus neutralization by a therapeutic antibody

West Nile virus is a mosquito-borne flavivirus closely related to the human epidemic-causing dengue, yellow fever and Japanese encephalitis viruses. In establishing infection these icosahedral viruses undergo endosomal membrane fusion catalysed by envelope glycoprotein rearrangement of the putative receptor-binding domain III (DIII) and exposure of the hydrophobic fusion loop. Humoral immunity has an essential protective function early in the course of West Nile virus infection. Here, we investigate the mechanism of neutralization by the E16 monoclonal antibody that specifically binds DIII. Structurally, the E16 antibody Fab fragment engages 16 residues positioned on four loops of DIII, a consensus neutralizing epitope sequence conserved in West Nile virus and distinct in other flaviviruses. The E16 epitope protrudes from the surface of mature virions in three distinct environments, and docking studies predict Fab binding will leave five-fold clustered epitopes exposed. We also show that E16 inhibits infection primarily at a step after viral attachment, potentially by blocking envelope glycoprotein conformational changes. Collectively, our results suggest that a vaccine strategy targeting the dominant DIII epitope may elicit safe and effective immune responses against flaviviral diseases.     

Lower Cambrian small shelly faunas from Zhejiang (China)and their biostratigraphical implications

Despite a long history of research on the Early Cambrian in China most available data on small skeletal fossils concern fossil associations of the shallow carbonate platform. Information on skeletal fossils from marginal shelf environments of the Yangtze Platform is scanty, which may reflect the rarity of fossils in deeper sedimentary environments but is also due to limitation of carbonate distribution and outcrops, difficulties in fossil extraction, and a general research focus on the Precambrian-Cambrian boundary beds on the carbonate platform. Here we present a documentation of Meishucunian to Qiongzhusian small skeletal fossils from the lower Hetang Formation and the chert unit at its base from the Jiangshan region, Zhejiang Province, representing a relatively deep shelf environment compared to the inner shelf region. The earliest association (Meishucunian) from the chert unit underlying the Hetang Formation is mainly characterized by the occurrence of Protohertzina anabarica, P. unguliformis, Fengzuella zhejiangensis, and Kaiyangites novilis, which differs somewhat in composition from SSF-associations of typical inner shelf deposits. The enigmatic skeletal fossil Fengzuella zhejiangensis, which exhibits an unusual secretional growth mode previously unrecognized from the Early Cambrian, is described in detail. A younger (Qiongzhusian) fossil association contains numerous arthropod remains, such as disarticulated spines of arthropods (Jiangshanodus- and Kijacus-type), which have previously been considered as conodont-like fossils, and bradoriid valves.     

Integer Programming Methods for Seriation and Unidemensional Scaling of Proximity Matrices: A Review and Some Extensions

L ₁-norm are also presented. I conclude that the computational scaling problems depends largely on the criterion of interest, with unidimensional scaling problems depends largely on the criterion of interest, with unidimensional scaling in the L ₁-norm being especially challenging.     

Small molecule activators of SIRT1 as therapeutics for the treatment of type 2 diabetes

Calorie restriction extends lifespan and produces a metabolic profile desirable for treating diseases of ageing such as type 2 diabetes. SIRT1, an NAD+-dependent deacetylase, is a principal modulator of pathways downstream of calorie restriction that produce beneficial effects on glucose homeostasis and insulin sensitivity. Resveratrol, a polyphenolic SIRT1 activator, mimics the anti-ageing effects of calorie restriction in lower organisms and in mice fed a high-fat diet ameliorates insulin resistance, increases mitochondrial content, and prolongs survival. Here we describe the identification and characterization of small molecule activators of SIRT1 that are structurally unrelated to, and 1,000-fold more potent than, resveratrol. These compounds bind to the SIRT1 enzyme-peptide substrate complex at an allosteric site amino-terminal to the catalytic domain and lower the Michaelis constant for acetylated substrates. In diet-induced obese and genetically obese mice, these compounds improve insulin sensitivity, lower plasma glucose, and increase mitochondrial capacity. In Zucker fa/fa rats, hyperinsulinaemic-euglycaemic clamp studies demonstrate that SIRT1 activators improve whole-body glucose homeostasis and insulin sensitivity in adipose tissue, skeletal muscle and liver. Thus, SIRT1 activation is a promising new therapeutic approach for treating diseases of ageing such as type 2 diabetes.     

Mechanochemical analysis of DNA gyrase using rotor bead tracking

DNA gyrase is a molecular machine that uses the energy of ATP hydrolysis to introduce essential negative supercoils into DNA. The directionality of supercoiling is ensured by chiral wrapping of the DNA around a specialized domain of the enzyme before strand passage. Here we observe the activity of gyrase in real time by tracking the rotation of a submicrometre bead attached to the side of a stretched DNA molecule. In the presence of gyrase and ATP, we observe bursts of rotation corresponding to the processive, stepwise introduction of negative supercoils in strict multiples of two. Changes in DNA tension have no detectable effect on supercoiling velocity, but the enzyme becomes markedly less processive as tension is increased over a range of only a few tenths of piconewtons. This behaviour is quantitatively explained by a simple mechanochemical model in which processivity depends on a kinetic competition between dissociation and rapid, tension-sensitive DNA wrapping. In a high-resolution variant of our assay, we directly detect rotational pauses corresponding to two kinetic substeps: an ATP-independent step at the end of the reaction cycle, and an ATP-binding step in the middle of the cycle, subsequent to DNA wrapping.