Initial characterization of the vitamin D binding protein (Gc-globulin) binding site on the neutrophil plasma membrane: evidence for a chondroitin sulfate proteoglycan.

The vitamin D binding protein (DBP) is a multifunctional plasma protein that can modulate certain immune and inflammatory responses. The diverse cellular functions of DBP appear to require cell surface binding to mediate these processes. Numerous reports have detected DBP bound to the surface of several cell types and would support the concept of a cell surface binding site for DBP. However, direct evidence for such a molecule has been lacking and essentially nothing is known about its basic biochemical properties. In the present study, radioiodinated DBP was used as a probe to characterize biochemically the neutrophil DBP binding site. Radiolabeled DBP binds to and remains associated with the plasma membrane and is not degraded. Quantitation of DBP binding to either intact cells or purified plasma membranes showed nonsaturable (linear) binding with positive cooperativity, possibly suggesting DBP oligomer formation. Solubilization of cell bound 125I-DBP with various nonionic and zwitterionic detergents demonstrated that DBP binds to a membrane macromolecule that partitions to the detergent insoluble fraction. Moreover, this molecule does not associate with the cytoskeleton. Cross-linking of radiolabeled DBP bound to plasma membranes increased the amount of protein that partitioned to the insoluble fraction, and analysis of these complexes by SDS-PAGE revealed that they may be very large since they did not enter the gel. Finally, treatment of plasma membranes with either proteases or chondroitinase ABC completely abrogated membrane binding of DBP, suggesting that the protein binds to a chondroitin sulfate proteoglycan.     

Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report

To investigate West Nile virus (WNV) circulation in rural populations in Gabon, we undertook a large serological survey focusing on human rural populations, using two different ELISA assays. A sample was considered positive when it reacted in both tests. A total of 2320 villagers from 115 villages were interviewed and sampled. Surprisingly, the WNV-specific IgG prevalence was high overall (27.2%) and varied according to the ecosystem: 23.7% in forested regions, 21.8% in savanna, and 64.9% in the lakes region. The WNV-specific IgG prevalence rate was 30% in males and 24.6% in females, and increased with age. Although serological cross-reactions between flaviviruses are likely and may be frequent, these findings strongly suggest that WNV is widespread in Gabon. The difference in WNV prevalence among ecosystems suggests preferential circulation in the lakes region. The linear increase with age suggests continuous exposure of Gabonese populations to WNV. Further investigations are needed to determine the WNV cycle and transmission patterns in Gabon.     

Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range

We have calibrated five different molecular clocks for circulating poliovirus based upon the rates of fixation of total substitutions (K(t)), synonymous substitutions (K(s)), synonymous transitions (A(s)), synonymous transversions (B(s)), and nonsynonymous substitutions (K(a)) into the P1/capsid region (2,643 nucleotides). Rates were determined over a 10-year period by analysis of sequences of 31 wild poliovirus type 1 isolates representing a well-defined phylogeny derived from a common imported ancestor. Similar rates were obtained by linear regression, the maximum likelihood/single-rate dated-tip method, and Bayesian inference. The very rapid K(t) [(1.03 +/- 0.10) x 10(-2) substitutions/site/year] and K(s) [(1.00 +/- 0.08) x 10(-2)] clocks were driven primarily by the A(s) clock [(0.96 +/- 0.09) x 10(-2)], the B(s) clock was approximately 10-fold slower [(0.10 +/- 0.03) x 10(-2)], and the more stochastic K(a) clock was approximately 30-fold slower [(0.03 +/- 0.01) x 10(-2)]. Nonsynonymous substitutions at all P1/capsid sites, including the neutralizing antigenic sites, appeared to be constrained by purifying selection. Simulation of the evolution of third-codon positions suggested that saturation of synonymous transitions would be evident at 10 years and complete at approximately 65 years of independent transmission. Saturation of synonymous transversions was predicted to be minimal at 20 years and incomplete at 100 years. The rapid evolution of the K(t), K(s), and A(s) clocks can be used to estimate the dates of divergence of closely related viruses, whereas the slower B(s) and K(a) clocks may be used to explore deeper evolutionary relationships within and across poliovirus genotypes.     

Biology and interactions of two distinct monopartite begomoviruses and betasatellites associated with radish leaf curl disease in India

Background

Emerging whitefly transmitted begomoviruses are major pathogens of vegetable and fibre crops throughout the world, particularly in tropical and sub-tropical regions. Mutation, pseudorecombination and recombination are driving forces for the emergence and evolution of new crop-infecting begomoviruses. Leaf curl disease of field grown radish plants was noticed in Varanasi and Pataudi region of northern India. We have identified and characterized two distinct monopartite begomoviruses and associated beta satellite DNA causing leaf curl disease of radish (Raphanus sativus) in India.

Results

We demonstrate that RaLCD is caused by a complex of two Old World begomoviruses and their associated betasatellites. Radish leaf curl virus-Varanasi is identified as a new recombinant species, Radish leaf curl virus (RaLCV) sharing maximum nucleotide identity of 87.7% with Tomato leaf curl Bangladesh virus-[Bangladesh:2] (Accession number AF188481) while the virus causing radish leaf curl disease-Pataudi is an isolate of Croton yellow vein mosaic virus-[India] (CYVMV-IN) (Accession number AJ507777) sharing 95.8% nucleotide identity. Further, RDP analysis revealed that the RaLCV has a hybrid genome, a putative recombinant between Euphorbia leaf curl virus and Papaya leaf curl virus. Cloned DNA of either RaLCV or CYVMV induced mild leaf curl symptoms in radish plants. However, when these clones (RaLCV or CYVMV) were individually co-inoculated with their associated cloned DNA betasatellite, symptom severity and viral DNA levels were increased in radish plants and induced typical RaLCD symptoms. To further extend these studies, we carried out an investigation of the interaction of these radish-infecting begomoviruses and their associated satellite, with two tomato infecting begomoviruses (Tomato leaf curl Gujarat virus and Tomato leaf curl New Delhi virus). Both of the tomato-infecting begomoviruses showed a contrasting and differential interaction with DNA satellites, not only in the capacity to interact with these molecules but also in the modulation of symptom phenotypes by the satellites.

Conclusion

This is the first report and experimental demonstration of Koch's postulate for begomoviruses associated with radish leaf curl disease. Further observations also provide direct evidence of lateral movement of weed infecting begomovirus in the cultivated crops and the present study also suggests that the exchange of betasatellites with other begomoviruses would create a new disease complex posing a serious threat to crop production.     

Circulation of endemic type 2 vaccine-derived poliovirus in Egypt from 1983 to 1993

From 1988 to 1993, 30 cases of poliomyelitis associated with poliovirus type 2 were found in seven governorates of Egypt. Because many of the cases were geographically and temporally clustered and because the case isolates differed antigenically from the vaccine strain, it was initially assumed that the cases signaled the continued circulation of wild type 2 poliovirus. However, comparison of sequences encoding the major capsid protein, VP1 (903 nucleotides), revealed that the isolates were related (93 to 97% nucleotide sequence identity) to the Sabin type 2 oral poliovirus vaccine (OPV) strain and unrelated (<82% nucleotide sequence identity) to the wild type 2 polioviruses previously indigenous to Egypt (last known isolate: 1979) or to any contemporary wild type 2 polioviruses found elsewhere. The rate and pattern of VP1 divergence among the circulating vaccine-derived poliovirus (cVDPV) isolates suggested that all lineages were derived from a single OPV infection that occurred around 1983 and that progeny from the initiating infection circulated for approximately a decade within Egypt along several independent chains of transmission. Complete genomic sequences of an early (1988) and a late (1993) cVDPV isolate revealed that their 5' untranslated region (5' UTR) and noncapsid- 3' UTR sequences were derived from other species C enteroviruses. Circulation of type 2 cVDPVs occurred at a time of low OPV coverage in the affected communities and ceased when OPV coverage rates increased. The potential for cVDPVs to circulate in populations with low immunity to poliovirus has important implications for current and future strategies to eradicate polio worldwide.     

Genetic co-regulation of galactose and melibiose utilization in Saccharomyces.

The gal3 mutation of Saccharomyces, which is associated with an impairment in the utilization of galactose, has been shown to be pleiotropic, causing similar impairments in the utilization of melibiose and maltose. Milibiose utilization and alpha-galactosidase production are directly controlled by the galactose regulatory elements i, c, and GAL4. The fermentation of maltose and the induction of alpha-glucosidase are regulated independently of the i, c, GAL4 system. The production of alpha-galactosidase and galactose-1-phosphate uridyl transferase is coordinate in galactokinaseless strains. Galactose serves as a nonmetabolized, gratuitous inducer of alpha-galactosidase in strains lacking the genes for one or more of the Leloir pathway enzymes.     

Crosslinking of phenylboronic acid receptors as a means of glucose selective holographic detection

A holographic sensor for the detection of glucose has been developed that is based on a hydrogel film containing phenylboronic acid receptors. Changes to the replay wavelength of the hologram were used to characterise the swelling and de-swelling behaviour of the hydrogel matrix upon receptor-ligand binding. The effect of introducing a fixed positive charge into the polymer matrix by modification of the hydrogel with a quaternary amine group (3-acrylamidopropyl)trimethylammonium chloride (ATMA), was investigated for a range of sugars and the alpha-hydroxy acid, lactate, at physiological pH. The quaternary amine-modified hydrogel matrix was found to contract in the presence of glucose, whereas, it was minimally responsive to other saccharides. The selectivity of the sensor for glucose compared to lactate was also significantly improved compared to the unmodified film. A crosslinking mechanism is proposed to explain the enhanced selectivity to glucose.     

UV radiation reduces epidermal cell expansion in Arabidopsis thaliana leaves without altering cellular microtubule organization

Upon chronic UV treatment pavement cell expansion in Arabidopsis leaves is reduced, implying alterations in symplastic and apoplastic properties of the epidermal cells. In this study, the effect of UV radiation on microtubule patterning is analysed, as microtubules are thought to serve as guiding rails for the cellulose synthase complexes depositing cellulose microfibrils. Together with hemicelluloses, these microfibrils are regarded as the load-bearing components of the cell wall. Leaves of transgenic plants with fluorescently tagged microtubules (GFP-TUA6) were as responsive to UV as wild type plants. Despite the UV-induced reduction in cell elongation, confocal microscopy revealed that cellular microtubule arrangements were seemingly not affected by the UV treatments. This indicates an unaltered deposition of cellulose microfibrils in the presence of UV radiation. Therefore, we surmise that the reduction in cell expansion in UV-treated leaves is most probably due to changes in cell wall loosening and/or turgor pressure.Key words: arabidopsis, cell expansion, GFP-TUA6, leaf development, microtubule cytoskeleton, UV radiationPhotosynthetic functions such as solar light capture and carbon fixation are highly evolved features of plant leaves. To fulfil these functions in an optimal way, leaf development needs to be tuned to environmental conditions. Leaves are continuously exposed and subjected to environmental influences, which serve as co-regulators of leaf and plant development.¹ This ability of plants to adapt, secures the plant''s survival, even under non-optimal conditions. An example of a regulatory environmental parameter is solar light, indispensable for photosynthesis but potentially causing photoinhibition and/or UV-radiation stress. The highly energetic ultraviolet B (UV-B) rays of short wavelengths (280–315 nm) can both cause damage, as well as induce a range of specific metabolic and morphogenic plant responses. It was reported before that exposure to low dose UV radiation reduces Arabidopsis leaf size due to a decreased cell size.² Expansion of leaf epidermal cells of Arabidopsis thaliana is the combined action of promotion and restriction of growth, resulting in the typical irregular sinuous pavement cells. It has been postulated that cellulose microfibrils are responsible for generating a force opposing isotropic expansion by creating neck regions in between outgrowing lobes.³ As the microtubule cytoskeleton is believed to serve as guiding rails for the cellulose synthase complexes (CESAs),⁴ the deposition of the cellulose fibrils is intimately linked to the cortical microtubule arrangement. We have studied the UV-effect on microtubule organisation in leaf epidermal cells whose expansion had decreased upon this UV radiation. Microtubules in the adaxial pavement cells of the fourth leaf were monitored on several successive days in a transgenic line containing GFP fused to tubulin A6.⁵ The chronic UV treatment was started on day 0 when the plants were 2 weeks old, using UV exposure conditions as described in reference ². First the responsiveness of the GFP-TUA6 plants to UV radiation was evaluated. Similar to wild type (WT) plants,² the GFP-TUA6 plants had smaller leaves following 8 days of UV treatment (t-test, p < 0.01) (Fig. 1). This was caused by a significant reduction in the generalized cell area average of all measured cells, irrespective of the location within the leaf (Fig. 1; t-test, p < 0.01). In more detail, the average cell area within the base, middle and top zones of the GFP-TUA6 leaf was systematically lower in UV-treated leaves from 8 days after the treatment started onwards (data not shown).Open in a separate windowFigure 1Effect of UV radiation on leaf and cell area after different days of UV radiation. Open asterisks indicate a statistically significant difference in leaf area between UV-treated and control plants, black asterisks indicate statistically significant difference in cell area (t-test, *p < 0.05, **p < 0.01, ***p < 0.001). Error bars indicate the standard error for five different leaves at all measured time-points and 600, 170 and 180 cells at day 0, 8 and 12 respectively.As GFP-TUA6 leaves were as responsive to UV radiation as wild type leaves, confocal microscopy was used to visualize the organisation of the cortical microtubules facing the outer periclinal wall of the adaxial epidermis. No clear difference in microtubule (re)organization could be detected during the development of pavement cells, and throughout the UV treatment period. As shown in Figure 2 at day 2, pavement cells with comparable areas are similarly shaped in control and UV-irradiated plants and contain similar microtubule arrangements (Fig. 2 and marked cells). This means that microtubule organization is not directly affected by the UV exposure and that shape development proceeds in an analoguous manner as under control conditions. This lack of alteration in the microtubule arrangement can be observed for cells at the leaf tip, which were already in the process of lobe formation at the start of the exposure period, as well as for cells at the leaf base. Under our growth conditions, and in the monitored leaf number 4, cell proliferation still took place in this part of the leaf and lobes only started to appear on the cell surface. As microtubules are linked to the deposition of cellulose microfibrils, it can be assumed that no alterations in cellulose deposition occur upon UV treatment either. We can therefore conclude that the process of lobe formation and microtubule patterning is not impeded and that only the extent of cell expansion is restricted upon UV exposure.Open in a separate windowFigure 2Microtubule pattern in control and UV-exposed leaves visualized using GFP-TUA6 and confocal microscopy. Both images are from cells at the mid zone of the fourth leaf at day 2. Microtubules are similarly arranged in equally shaped and sized cells of control and UV-exposed leaves. The marked cells show a pattern whereby the tubules are centred in the neck regions between two outgrowing lobes.According to the Lockhart equation,⁶ cell (wall) growth is modulated by wall biomechanics and turgor pressure. Concerning turgor pressure, no clear differences in this factor between UV-exposed and control plants of Lactuca sativa L.⁷ and Pisum sativum⁸ could be observed, reinforcing the idea that especially the modulation of cell wall properties is the main factor causing the observed UV-induced reduction in cell expansion. Some reports indicate differential expression of wall loosening enzymes like expansins or xyloglucan endotransglycosylase/hydrolases (XTHs),^9,10 or cell wall strengthening enzymes as particular peroxidases⁷ after UV exposure. Another key event could involve UV-mediated changes in the phenylpropanoid pathway, which may cause changes in the lignin biosynthesis. As shown by the literature^11–14 lignin may well be an important modulator of cell wall architecture in Arabidopsis and therefore alterations in lignin synthesis could form the basis for morphological modifications. Further research on the cell wall properties of UV-treated plants may resolve this uncertainty.As a general conclusion we can state that the patterning of microtubules is not altered, but that alterations in cell wall composition or arrangements are the most plausible candidates for the observed reduction in pavement cell expansion upon chronic UV treatment.     

Diagnosis of Primary Cancer of the Liver

The diagnosis of primary cancer of the liver was reviewed in 75 patients. A definitive diagnosis was made during life in 63% and in a further 20% this condition was suspected though histological confirmation was obtained only at necropsy. The most common presenting complaints were abdominal pain and weight loss and the most frequent findings hepatomegaly and ascites. Less than one-half of the patients were jaundiced and when present it was usually mild. An arterial bruit was heard over the liver in 25% of the patients. A sudden and unexplained deterioration in a patient known to have cirrhosis or haemochromatosis should raise the possibility of a primary hepatic tumour; this occurred in 24% of our patients.Alpha-fetoprotein was found in the serum of 11 out of 18 cases. The presence of a mass in the liver was frequently confirmed by liver scan, portal venography, or hepatic arteriography, but these showed no features diagnostic of a primary tumour. Liver scan also proved useful in localizing the lesion for biopsy purposes. Definitive diagnosis is dependent on the histological demonstration of the features of the tumour. This can frequently be achieved by percutaneous needle biopsy, which was positive in 38 out of 57 patients. Wedge biopsies were positive in a further nine patients.     

Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons

Replicative fitness of poliovirus can be modulated systematically by replacement of preferred capsid region codons with synonymous unpreferred codons. To determine the key genetic contributors to fitness reduction, we introduced different sets of synonymous codons into the capsid coding region of an infectious clone derived from the type 2 prototype strain MEF-1. Replicative fitness in HeLa cells, measured by plaque areas and virus yields in single-step growth experiments, decreased sharply with increased frequencies of the dinucleotides CpG (suppressed in higher eukaryotes and most RNA viruses) and UpA (suppressed nearly universally). Replacement of MEF-1 capsid codons with the corresponding codons from another type 2 prototype strain (Lansing), a randomization of MEF-1 synonymous codons, increased the %G+C without increasing CpG, and reductions in the effective number of codons used had much smaller individual effects on fitness. Poliovirus fitness was reduced to the threshold of viability when CpG and UpA dinucleotides were saturated within and across synonymous codons of a capsid region interval representing only ∼9% of the total genome. Codon replacements were associated with moderate decreases in total virion production but large decreases in the specific infectivities of intact poliovirions and viral RNAs. Replication of codon replacement viruses, but not MEF-1, was temperature sensitive at 39.5°C. Synthesis and processing of viral intracellular proteins were largely unaltered in most codon replacement constructs. Replacement of natural codons with synonymous codons with increased frequencies of CpG and UpA dinucleotides may offer a general approach to the development of attenuated vaccines with well-defined antigenicities and very high genetic stabilities.Diversification of genomic sequences is constrained in all biological systems. At the level of primary sequences, the range of variability in coding regions is restricted by the codon usage bias (CUB), whereby a subset of synonymous codons are preferentially used in translation (24, 53, 69). The intensity of the CUB and the specific set of preferred codons vary widely across biological systems (39). Intertwined with the CUB is the suppression of the dinucleotides CpG and TpA (or UpA in RNA viruses) in the genomes of higher eukaryotes (4, 7, 26, 61) and many of their RNA viruses and small DNA viruses (28, 49). Variation in the primary sequences of RNA virus genomes is further constrained by requirements to maintain essential secondary and higher-order structures (42, 54, 68).We previously described the modulation of the replicative fitness of the Sabin type 2 oral poliovirus vaccine (OPV) strain (Sabin 2) by systematically changing the CUB in the capsid region, replacing the naturally occurring preferred codons with an unpreferred synonymous codon (isocodon) for each of nine amino acids (8). We called our approach “codon deoptimization” to contrast with the process of codon optimization, which is frequently used to maximize expression of foreign proteins in heterologous host systems (1, 27, 70). Apart from its potential application to development of improved poliovirus vaccines (8, 13, 38), experimental investigations of codon deoptimization directly test the relationships between replicative fitness, the extent of CUB, and the intensity of CpG and UpA suppression. As a model system for such studies, polioviruses offer several favorable properties, including (i) intrinsically high error rates for the poliovirus RNA-dependent RNA polymerase (2, 14, 16, 65), (ii) very high evolution rates (25), (iii) short generation times (8 to 10 h) and large progeny yields of prototype polioviruses, and (iv) well-developed reverse genetics (9).In this report, we extend our codon deoptimization strategy to the type 2 wild poliovirus prototype strain MEF-1. As before, we restricted our replacement of synonymous codons to the capsid coding region, which encodes two of the defining properties of polioviruses, namely, (i) the capacity to bind the CD155 poliovirus receptor (PVR) (23) and (ii) the poliovirus type-specific neutralizing antigenic sites (35). No changes were made to the flanking 5′-untranslated region and noncapsid region sequences, as they contain essential secondary structural elements (42, 54, 68) and are frequently exchanged out by recombination during circulation of poliovirus in human populations (20, 30, 32). MEF-1 was selected because of its high fitness level (hence, its use as the type 2 component of the inactivated poliovirus vaccine [IPV]) and because of its neurovirulence for humans (15), for nontransgenic mice (52), and for transgenic mice expressing the PVR (71). Type 2 polioviruses were selected first for study because the Sabin 2 OPV strain is most frequently associated with vaccine-associated paralytic poliomyelitis in contacts of OPV recipients (57, 59), with prolonged excretion of immunodeficiency-associated vaccine-derived polioviruses (VDPVs) (10, 31, 60), and with the emergence of circulating VDPVs in areas of low OPV coverage (10, 31).Consistent with our previous findings, the fitness of MEF-1 decreased in proportion to the total number of synonymous replacement codons. Fitness was reduced most efficiently by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous codons. Saturation of CpG and UpA in a small capsid interval (representing only ∼9% of the genome) reduced fitness to the threshold of viability, even though the MEF-1 amino acid sequence was unaltered. The most prominent biological effect of deoptimization of codon usage and the large-scale incorporation of CpG and UpA was a sharp reduction in virus specific infectivities. In contrast, translation and processing of viral proteins and yields of intact virus particles with native antigenicities were reduced only moderately by increased CpG and UpA frequencies. Codon deoptimization with concurrent increases in the frequencies of CpG and/or UpA dinucleotides in RNA virus genomes may provide a novel general approach to the rational design of improved attenuated vaccines with predictable and stable genetic properties.