Penicillin-binding proteins 4 and 5 of Haemophilus influenzae are involved in cell wall incorporation

Abstract Permeabilized cells of Haemophilus influenzae incorporate wall precursors into murein material in an ampicillin-sensitive reaction. In resistant transformants that contain the low antibiotic affinity penicillin-binding proteins (PBPs) 4 and 5, the sensitivity of this incorporation reaction to ampicillin is proportionally lower, suggesting a catalytic role for these proteins in wall synthesis. We conclude that, analogous to the reaction in Escherichia coli , PBPs 4 and 5 of H. influenzae have transpeptidase activity.     

Natural incorporation of mercury in bone

Mercury (Hg) is a highly toxic element that causes bone defects and malformations. Structure and surface analyses using quantitative x-ray diffraction using the Rietveld method, High-Resolution Transmission Electron Microscopy and nanodiffraction analyses, and Fourier-Transformed Infrared spectroscopy showed that bone enriched naturally with Hg (≤ 2.3 %) contained Hg₃PO₄ [(Hg₂)₃(PO₄)₂] and HgO. Bone [mostly as apatite, verified as carboxyapatite Ca₁₀(PO₄)₄(CO₃)₃(OH)₂(s)] and cinnabar (HgS) dissolved releasing Hg⁺ (existing as dimer Hg₂²⁺) and PO₄³⁻, both of which became immobilized as (Hg₂)₃(PO₄)₂. Besides, released Hg²⁺ became oxidized to form HgO. The outcome of this work is novel, provided that only a handful of stable compounds of Hg₂²⁺ are found in nature.     

The transient and constitutive inflammatory signaling in tumorigenesis

Comment on: Rokavec M, et al. Mol Cell 2012; 45:777-89.     

Generation of a purely clonal defective interfering influenza virus

Defective interfering (DI) influenza viruses carry a large deletion in a gene segment that interferes with the replication of infectious virus; thus, such viruses have potential for antiviral therapy. However, because DI viruses cannot replicate autonomously without the aid of an infectious helper virus, clonal DI virus stocks that are not contaminated with helper virus have not yet been generated. To overcome this problem, we used reverse genetics to generate a clonal DI virus with a PB2 DI gene, amplified the clonal DI virus using a cell line stably expressing the PB2 protein, and confirmed its ability to interfere with infectious virus replication in vitro. Thus, our approach is suitable for obtaining purely clonal DI viruses, will contribute to the understanding of DI virus interference mechanisms and can be used to develop DI virus‐based antivirals.     

Semiparametric Regression in Size-Biased Sampling

Summary .  Size-biased sampling arises when a positive-valued outcome variable is sampled with selection probability proportional to its size. In this article, we propose a semiparametric linear regression model to analyze size-biased outcomes. In our proposed model, the regression parameters of covariates are of major interest, while the distribution of random errors is unspecified. Under the proposed model, we discover that regression parameters are invariant regardless of size-biased sampling. Following this invariance property, we develop a simple estimation procedure for inferences. Our proposed methods are evaluated in simulation studies and applied to two real data analyses.     

Site-Specific Structural Variations Accompanying Tubular Assembly of the HIV-1 Capsid Protein

The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurements on HIV-1 CA tubes that provide new information regarding changes in molecular structure that accompany CA self-assembly, local dynamics within CA tubes, and possible mechanisms for the generation of lattice curvature. This information is contained in site-specific assignments of signals in two- and three-dimensional solid-state NMR spectra, conformation-dependent ¹⁵N and ¹³C NMR chemical shifts, detection of highly dynamic residues under solution NMR conditions, measurements of local variations in transverse spin relaxation rates of amide ¹H nuclei, and quantitative measurements of site-specific ¹⁵N–¹⁵N dipole–dipole couplings. Our data show that most of the CA sequence is conformationally ordered and relatively rigid in tubular assemblies and that structures of the N-terminal domain (NTD) and the C-terminal domain (CTD) observed in solution are largely retained. However, specific segments, including the N-terminal β-hairpin, the cyclophilin A binding loop, the inter-domain linker, segments involved in intermolecular NTD–CTD interactions, and the C-terminal tail, have substantial static or dynamical disorder in tubular assemblies. Other segments, including the 3₁₀-helical segment in CTD, undergo clear conformational changes. Structural variations associated with curvature of the CA lattice appear to be localized in the inter-domain linker and intermolecular NTD–CTD interface, while structural variations within NTD hexamers, around local 3-fold symmetry axes, and in CTD–CTD dimerization interfaces are less significant.     

Sequences of cDNAs for human salivary and pancreatic α-amylases

The nucleotide sequences of the cloned human salivary and pancreatic α-amylase cDNAs correspond to the continuous mRNA sequences of 1768 and 1566 nucleotides, respectively. These include all of the amino acid coding regions. Salivary cDNA contains 200 bp in the 5′-noncoding region and 32 in the 3′-noncoding region. Pancreatic cDNA contains 3 and 27 bp of 5′- and 3′-noncoding regions, respectively. The nucleotide sequence humology of the two cDNAs is 96% in the coding region, and the predicted amino acid sequences are 94% homologous.Comparison of the sequences of human α-amylase cDNAs with those previously obtained for mouse α-amylase genes (Hagenbuchle et al., 1980; Schibler et al., 1982) showed the possibility of gene conversion between the two genes of human α-amylase.     

A comparison of vector population indices for forecasting barley yellow dwarf virus in autumn sown cereal crops

Two approaches based on the concept of a vector population index are considered as possible deterministic elements for an empirical forecast of barley yellow dwarf virus (BYDV) in autumn sown cereals. The first, an aerial vector index, is a further elaboration of the infectivity index proposed by Plumb, Lennon & Gutteridge (1981), which assumes that virus damage is a function of the number of infective migrant alatae of the two main aphid vectors, Rhopalosiphum padi L. and Sitobion avenae F., integrated over time from crop planting or emergence. The new formulation, however, excludes holocyclic alate morphs (i.e. males and gynoparae) of the former species, which, although generally abundant in autumn, are nevertheless perceived as relatively unimportant virus vectors since they colonise only the alternative woody host, Prunus padus (the bird-cherry tree). The second approach, a crop vector index, is a more fundamental departure which argues that field populations of viruliferous aphids, both alatae and apterae, which have already colonised cereals, may be a better criterion of potential virus spread than the density of aerial migrant vectors. This index retains a similar integral form, but evaluates crop exposure to BYDV as accumulated infectious aphid-days. A method is described whereby this function can be derived from irregular or infrequent aphid samples in the crop. Both methods, unlike Plumb's (1976) original concept, produced indices which were significantly related to subsequent virus infection and yield loss in winter barley at Long Ashton (S.W. England, UK), 1978–1986. The best models were obtained with the crop vector index, fitted to observed virus infection by generalised linear regression using a complementary log-log link function, or to observed yield loss by simple linear regression using a log transformation of yield (r = 0.84 in each case; compared with r-values > 0.65 for the aerial vector index, and > 0.35 for Plumb's (1976) index). However, the residual errors and hence confidence limits of these fitted regressions were too large for predicting damage that was significantly less than a reasonable economic damage threshold for BYDV control. Analyses of the separate components of each index showed a good general relationship between aphid infectivity and the severity of crop infection, confirming the epidemiological importance of this factor. The functional expressions of aphid density, however, were not significant. This evident weakness in the models, and alternative approaches to BYDV forecasting are discussed.