Evidence for post-translational glycosylation of a nonglycosylated precursor protein of herpes simplex virus type 1.

Incubation of herpes simplex virus type 1-infected Vero and HEp-2 cells at a reduced temperature (34 degrees C) enhanced the detection of the nonglycosylated precursors (pgB97 and pgC75) to the gB and gC glycoproteins in the cytoplasmic and nuclear fractions. Relative to the fully glycosylated and high-mannose forms detected, the nonglycosylated precursors were the predominant components associated with the nuclear fraction of infected cells. Furthermore, addition of protease inhibitors to the fractionation buffers did not affect the distribution or abundance of the nonglycosylated precursors, suggesting that the presence of pgB97 and pgC75 was not the result of proteolysis. When infected Vero or HEp-2 cells were harvested at various times postinfection, the nonglycosylated precursors were detected after the initial appearance of the high mannose components (pgB110 and pgC105). In Vero cells, pgB97 and pgC75 were detected simultaneously at 8 h postinfection, whereas detection was not apparent in HEp-2 cells until 20 h postinfection. Conditions which favored detection of appreciable amounts of nonglycosylated precursors provided an unique approach to probe possible post-translational modifications in the absence of inhibitors of glycosylation. In nuclear fractions isolated from cycloheximide-treated HEp-2 or Vero cells, numerous discrete gC-immunoreactive bands migrating with decreased electrophoretic mobility relative to the nonglycosylated precursor pgC75 were observed. This series of one to four additional bands was eliminated by digestion with endoglycosidase H, and the appearance of these bands was blocked by the addition of tunicamycin. Collectively, the data suggest that high-mannose core oligosaccharides may be added to the nonglycosylated precursor of the gC glycoprotein of herpes simplex virus type 1 in a post-translational fashion.     

The detection,accumulation and stabilization of a tetrahedral intermediate in trypsin catalysis

The reaction of trypsin with N^α-carbobenzoxy-L-lysine p-nitroanilide has been studied in the 0 to ?60°C temperature region, over a wide range of pH^★ values, using aqueous-dimethyl sulfoxide cryosolvent. Spectrophotometric and kinetic evidence for the detection and stabilization of a tetrahedral intermediate is presented. The rate of formation of this intermediate, and the concentration accumulated, were pH^★-dependent. At pH^★ ≤ 6 (< ?40°C) essentially no tetrahedral adduct is formed or accumulated. Instead another intermediate, resembling the substrate in its spectral properties, is detected.     

How inhibiting nitrification affects nitrogen cycle and reduces environmental impacts of anthropogenic nitrogen input

Anthropogenic activities, and in particular the use of synthetic nitrogen (N) fertilizer, have doubled global annual reactive N inputs in the past 50–100 years, causing deleterious effects on the environment through increased N leaching and nitrous oxide (N₂O) and ammonia (NH₃) emissions. Leaching and gaseous losses of N are greatly controlled by the net rate of microbial nitrification. Extensive experiments have been conducted to develop ways to inhibit this process through use of nitrification inhibitors (NI) in combination with fertilizers. Yet, no study has comprehensively assessed how inhibiting nitrification affects both hydrologic and gaseous losses of N and plant nitrogen use efficiency. We synthesized the results of 62 NI field studies and evaluated how NI application altered N cycle and ecosystem services in N‐enriched systems. Our results showed that inhibiting nitrification by NI application increased NH₃ emission (mean: 20%, 95% confidential interval: 33–67%), but reduced dissolved inorganic N leaching (?48%, ?56% to ?38%), N₂O emission (?44%, ?48% to ?39%) and NO emission (?24%, ?38% to ?8%). This amounted to a net reduction of 16.5% in the total N release to the environment. Inhibiting nitrification also increased plant N recovery (58%, 34–93%) and productivity of grain (9%, 6–13%), straw (15%, 12–18%), vegetable (5%, 0–10%) and pasture hay (14%, 8–20%). The cost and benefit analysis showed that the economic benefit of reducing N's environmental impacts offsets the cost of NI application. Applying NI along with N fertilizer could bring additional revenues of $163 ha^?1 yr^?1 for a maize farm, equivalent to 8.95% increase in revenues. Our findings showed that NIs could create a win‐win scenario that reduces the negative impact of N leaching and greenhouse gas production, while increases the agricultural output. However, NI's potential negative impacts, such as increase in NH₃ emission and the risk of NI contamination, should be fully considered before large‐scale application.     

Interactions between pollinator and non‐pollinator fig wasps: correlations between their numbers can be misleading

Ficus and their species–specific pollinator fig wasps represent an obligate plant–insect mutualism, but figs also support a community of non‐pollinating fig wasps (NPFWs) that consist of phytophages and parasitoids or inquilines. We studied interactions between Kradibia tentacularis, the pollinator of a dioecious fig tree species Ficus montana, and an undescribed NPFW Sycoscapter sp. Members of Sycoscapter sp. oviposited 2–4 weeks after pollinator oviposition, when host larvae were present in the figs. No negative correlation was found between the numbers of the two wasp species emerging from figs in a semi‐natural population. However, in experiments where the numbers of pollinator foundresses entering a fig were controlled, Sycoscapter sp. significantly reduced the numbers of pollinator offspring. Consequently, it can be concluded that Sycoscapter sp. is a parasitoid of K. tentacularis (which may also feed on plant tissue). Sycoscapter females concentrate their oviposition in figs that contain more potential hosts, rendering invalid conclusions based on simple correlations of host and natural enemy numbers.     

Evidence against regulation of AMP-activated protein kinase and LKB1/STRAD/MO25 activity by creatine phosphate

Muscle contraction results in phosphorylation and activation of the AMP-activated protein kinase (AMPK) by an AMPK kinase (AMPKK). LKB1/STRAD/MO25 (LKB1) is the major AMPKK in skeletal muscle; however, the activity of LKB1 is not increased by muscle contraction. This finding suggests that phosphorylation of AMPK by LKB1 is regulated by allosteric mechanisms. Creatine phosphate is depleted during skeletal muscle contraction to replenish ATP. Thus the concentration of creatine phosphate is an indicator of cellular energy status. A previous report found that creatine phosphate inhibits AMPK activity. The purpose of this study was to determine whether creatine phosphate would inhibit 1) phosphorylation of AMPK by LKB1 and 2) AMPK activity after phosphorylation by LKB1. We found that creatine phosphate did not inhibit phosphorylation of either recombinant or purified rat liver AMPK by LKB1. We also found that creatine phosphate did not inhibit 1) active recombinant alpha1beta1gamma1 or alpha2beta2gamma2 AMPK, 2) AMPK immunoprecipitated from rat liver extracts by either the alpha1 or alpha2 subunit, or 3) AMPK chromatographically purified from rat liver. Inhibition of skeletal muscle AMPK by creatine phosphate was greatly reduced or eliminated with increased AMPK purity. In conclusion, these results suggest that creatine phosphate is not a direct regulator of LKB1 or AMPK activity. Creatine phosphate may indirectly modulate AMPK activity by replenishing ATP at the onset of muscle contraction.     

Class III Phosphatidylinositol 4-Kinase Alpha and Beta Are Novel Host Factor Regulators of Hepatitis C Virus Replication

Host factor pathways are known to be essential for hepatitis C virus (HCV) infection and replication in human liver cells. To search for novel host factor proteins required for HCV replication, we screened a subgenomic genotype 1b replicon cell line (Luc-1b) with a kinome and druggable collection of 20,779 siRNAs. We identified and validated several enzymes required for HCV replication, including class III phosphatidylinositol 4-kinases (PI4KA and PI4KB), carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD), and mevalonate (diphospho) decarboxylase. Knockdown of PI4KA could inhibit the replication and/or HCV RNA levels of the two subgenomic genotype 1b clones (SG-1b and Luc-1b), two subgenomic genotype 1a clones (SG-1a and Luc-1a), JFH-1 genotype 2a infectious virus (JFH1-2a), and the genomic genotype 1a (FL-1a) replicon. In contrast, PI4KB knockdown inhibited replication and/or HCV RNA levels of Luc-1b, SG-1b, and Luc-1a replicons. The small molecule inhibitor, PIK93, was found to block subgenomic genotype 1b (Luc-1b), subgenomic genotype 1a (Luc-1a), and genomic genotype 2a (JFH1-2a) infectious virus replication in the nanomolar range. PIK93 was characterized by using quantitative chemical proteomics and in vitro biochemical assays to demonstrate PIK93 is a bone fide PI4KA and PI4KB inhibitor. Our data demonstrate that genetic or pharmacological modulation of PI4KA and PI4KB inhibits multiple genotypes of HCV and represents a novel druggable class of therapeutic targets for HCV infection.Hepatitis C virus (HCV) causes liver disease in humans, including chronic hepatitis, cirrhosis, and hepatocellular carcinoma (52). The HCV genome is a single-stranded RNA molecule where both the 5′ and the 3′ untranslated region (UTR) contain highly conserved RNA structures necessary for polyprotein translation and genome replication (43). The processed polyprotein yields at least three structural proteins and six nonstructural proteins. The structural proteins include the core, which forms the viral nucleocapsid, and the envelope glycoproteins E1 and E2. The viral proteins processed by signal peptidases form viral particles that assemble at the endoplasmic reticulum (ER) and/or Golgi bodies and are released from the host cell by viral budding. The structural protein coding regions are separated from nonstructural proteins by the short membrane peptide p7, thought to function as an ion channel (43, 53). The nonstructural proteins NS2, NS3/4A, NS5A, and NS5B are involved in coordinating the intracellular processes of the virus life cycle, including polyprotein processing and viral RNA replication (34).The Luc-1b cell is a human hepatoma cell line (Huh7) that contains a genotype 1b HCV subgenomic replicon, a luciferase reporter, and a neomycin selection marker, allowing HCV replication to be studied both in vitro and in vivo (8, 36). This subgenomic replicon lacks the coding regions for NS2 and the structural proteins but contains the nonstructural proteins in cis, which are required for replication of the viral RNA. Expression of the luciferase gene acts as a surrogate marker for levels of HCV RNA produced in the cell. The goal of the present study was to use this subgenomic HCV replicon to screen siRNA libraries and identify novel host proteins that are involved in HCV replication.A number of cellular pathways and proteins that play critical roles in HCV replication have recently been described (41, 42, 46). In particular, replication of HCV is tied closely to its localization and transport to various internal membranes and to lipid metabolism (2). Most of the HCV proteins appear to be targeted to the surface of the ER and replication complexes appear to be transported to lipid rafts, where RNA replication can occur (2). Infectious virus particle formation occurs in association with lipid droplets, and this process requires the core and NS5A proteins. In addition, cholesterol pathway production of geranylgeranyl-PP is important to geranylate the FBL2 protein, which serves as a membrane anchor for NS5A (62). The hVAP proteins involved in the localization and trafficking between internal membranous structures are known to be associated with the HCV proteins NS5A and NS5B (59). Thus, host factor lipid metabolism and intracellular protein transport are necessary for HCV replication in cells.Targeting host factors that are required for viral replication offers a strategy to overcome viral resistance and may allow treatment for more than one genotype of HCV and/or a related Flaviviridae virus such as Dengue, West Nile, or yellow fever virus. The current standard-of-care treatment for the genotype 1 strain of HCV infection is pegylated interferon alpha plus ribavirin over a 6-month time course with more than half of infected patients being refractory to this treatment (57). In addition to genotype 1, there are at least five naturally occurring genotype variants of HCV that can complicate a patient''s response to therapy when infected with more than one genotype. As well as the development of mutations, the presence of multiple variants coexisting in patients is thought to contribute to the rapid development of resistance (40). A variety of antiviral therapeutic strategies aim to inhibit viral proteins directly with small molecules or siRNAs (13, 31, 33). Although some small molecule approaches have been successful in preclinical studies, small-molecule strategies directed against the viral targets can still be rendered ineffective due to the development of mutant, treatment-resistant viral strains (13, 40). Thus, combination therapies are a necessary approach to treat the many variants of HCV that exist in the patient population.In the present study, a set of 779 SMARTpool small interfering RNAs (siRNAs) targeting the kinome and 4 siRNAs targeting 5,000 druggable genes (20,000 siRNAs) were tested for their ability to block replication of the Luc-1b HCV subgenomic replicon. siRNAs targeting CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase), a tripartite enzyme that catalyzes the first three steps of pyrimidine biosynthesis, inhibited both the Luc-1b replicon and JFH1-2a virus expression. This activity is consistent with the known inhibitor of this enzyme, leflunomide, which has been shown previously to inhibit both respiratory syncytial virus and HCV (12, 54). siRNAs targeting the mevalonate (diphospho) decarboxylase (MVD) enzyme, which catalyzes the formation of mevalonate, were found to inhibit Luc-1b replication (19). Inhibition of the cholesterol biosynthesis pathway and host cell geranylation has been previously reported to inhibit HCV subgenomic replication (3, 24, 51, 62, 67). siRNA-mediated knockdown of the class III phosphatidylinositol 4-kinases PI4KA and PI4KB inhibited luciferase expression not only for the genotype 1b subgenomic replicons (Luc-1a and Luc-1b) but also for the viral RNA levels of SG-1b, Luc-1b, and Luc-1a. PI4KA knockdown also inhibited Renilla expression in the JFH-1 genotype 2a infectious virus (JFH1-2a), genotype 2a subgenomic replicon (SG-1a), and a genomic and subgenomic genotype 1a replicon (FL-1a and SG-1a). Using the small-molecule inhibitor PIK93 in compound affinity competition experiments and in vitro biochemical assays, we demonstrated PIK93 could bind and inhibit both PI4KA and PI4KB enzymatic activity (58). PIK93 could inhibit luciferase expression in the Luc-1b, Luc-1a, and JFH1-2a infectious virus assays in the submicromolar range. Together, our data suggest that PI4KA and PI4KB regulate HCV replication and that pharmacological inhibition of these enzymes represents a new class of antiviral agents for multiple genotypes of HCV. Finally, since PI4KA and PI4KB are known to regulate protein and lipid transport to and from the ER and Golgi bodies, their function may hold clues as to how movement of HCV replication complexes throughout different organelles is regulated.     

Comparative effects of interferon alpha‐2b and pegylated interferon alpha‐2b on menstrual cycles and ovarian hormones in cynomolgus monkeys

BACKGROUND : The covalent modification of interferon (IFN) α2b with monomethyoxy polyethylene glycol (PEG) reduces its clearance rate and increases its half‐life. High doses of interferon (IFN) α2b have previously been shown to affect maintenance of pregnancy in rhesus monkeys. Given the role of ovarian hormones in reproductive function and pregnancy, this study was conducted to assess the effects of PEG‐IFNα2b or IFNα2b (comparative control) on ovarian hormones and menstrual cyclicity in cynomolgus monkeys. In addition, the potential for reversibility of PEG‐IFNα2b or IFNα2b‐related observations was assessed. METHODS : Monkeys were administered 3,105 µg/m² human recombinant (hr) IFNα2b or 52, 262, or 4,239 µg/m² PEG‐hr‐IFNα2b every other day for one menstrual cycle, followed by a post‐dose period of up to two menstrual cycles. RESULTS : Monkeys administered 3,105 µg/m² hr‐IFNα2b or 52, 262, or 4,239 µg/m² PEG‐hr‐IFNα2b exhibited transient decreases in food consumption, leukocyte and erythrocyte parameters. Monkeys administered 3,105 µg/m² hr‐IFNα2b exhibited lengthened menstrual cycles that were associated with a delay in reaching peak ovarian hormone levels and lower respective peak concentrations. Similarly, monkeys administered 4,239 µg/m² PEG‐hr‐IFNα2b exhibited lengthened menstrual cycles and a delay in reaching peak ovarian hormone levels and slightly lower respective peak concentrations. Post‐dosing menstrual cycle length, estradiol and progesterone profiles exhibited evidence of recovery in both the hr‐IFNα2b and the high‐dose PEG‐hr‐IFNα2b groups. CONCLUSIONS : Administration of hr‐IFNα2b or PEG‐hr‐IFNα2b at high doses to cynomolgus monkeys resulted in similar effects on menstrual cycles, estradiol and progesterone profiles, and exhibited evidence of reversibility upon cessation of dosing. These results suggest that the previously observed high‐dose IFNα‐related effects on the maintenance of pregnancy in monkeys are likely the result of altered ovarian function. Birth Defects Res (Part B) 86:29‐39, 2009. © 2009 Wiley‐Liss, Inc.     

Spatial patterns of P fractions and chemical properties in soils of two native shrub communities in Senegal

Two shrub species (Piliostigma reticulatum (D.C.) Hochst (Caesalpinioideae) and Guiera senegalensis J.F. Gmel (Combretaceae) are commonly found in farmers’ fields at varying densities in semi-arid Senegal and throughout the Sahel where soils have chronically low phosphorus (P) availability. It seems plausible that shrub litter and the rhizospheres could influence P fractions and other chemical soil properties that affect crop productivity. Thus, a study was done at two sites, on the distribution of inorganic and organic soil P pools, organic C levels, and pH in soil beneath and outside the canopies of P. reticulatum and G. senegalensis (0-30 cm depth). Both sites had low total P ranging from 64 mg P kg^?1 to 135 mg P kg^-1, and low extractable PO₄ (resin Pi) (1–6 mg P kg^?1) with P fractions dominated by NaOH-P. Organic P (Po) made up about 50% of total P, and most of the organic P (>60%) was found in the NaOH-P fractions. The labile P, particularly bicarb-Po was higher in soil beneath shrub canopies (8.4 mg P kg ^?1), than outside the canopy (6.2 mg P kg ^?1). Similarly, C, N and P to a lesser extent, were more concentrated beneath shrub canopies. P. reticulatum soil was dominated by the NaOH-Po fraction, whereas G. senegalensis had higher bicarb-Po at one of the study sites. An index of biologically available organic P (Bicarb-Po) / (Bicarb-Po?+?Bicar-Pi?+?Resin Pi) was ?>?60% and indicates that biological processes represent an important part of P cycling in these shrub ecosystems. The differential ability of shrubs in modifying soil chemical properties under their canopies has major implications for biogeochemical cycling of nutrients and C in sandy soils of semi arid Sahelian ecosystems.