Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs

RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m5C) modifications is Tombo, which uses an "Alternative Model" to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa including viruses, bacteria, fungi, and animals. The algorithm consistently identified a m5C at the central position of a GCU motif. However, it also identified a m5C in the same motif in fully unmodified in vitro transcribed RNA, suggesting that this is a frequent false prediction. In the absence of further validation, several published predictions of m5C in a GCU context should be reconsidered, including those from human coronavirus and human cerebral organoid samples.

Host Derivation of Sindbis Virus Influences Mammalian Type I Interferon Response to Infection

Arboviruses are defined by their ability to replicate in both mosquito vectors and mammalian hosts. There is good evidence that arboviruses "prime" their progeny for infection of the next host, such as via differential glycosylation of their outer glycoproteins or packaging of host ribosomal subunits. We and others have previously shown that mosquito-derived viruses more efficiently infect mammalian cells than mammalian-derived viruses. These observations are consistent with arboviruses acquiring host-specific adaptations, and we hypothesized that a virus derived from either the mammalian host or mosquito vector elicits different responses when infecting the mammalian host. Here, we perform an RNA-sequencing analysis of the transcriptional response of Human Embryonic Kidney 293 (HEK-293) cells to infection with either mosquito (Aedes albopictus, C7/10)- or mammalian (Baby Hamster Kidney, BHK-21)-derived Sindbis virus (SINV). We show that the C7/10-derived virus infection leads to a more robust transcriptional response in HEK-293s compared to infection with the BHK-derived virus. Surprisingly, despite more efficient infection, we found an increase in interferon-β (IFN-β) and interferon-stimulated gene (ISG) transcripts in response to the C7/10-derived virus infection versus the BHK-derived virus infection. However, translation of interferon-stimulated genes was lower in HEK-293s infected with the C7/10-derived virus, starkly contrasting with the transcriptional response. This inhibition of ISG translation is reflective of a more rapid overall shut-off of host cell translation following infection with the C7/10-derived virus. Finally, we show that the C7/10-derived virus infection of HEK-293 cells leads to elevated levels of phosphorylated eukaryotic translation elongation factor-2 (eEF2), identifying a potential mechanism leading to the more rapid shut-off of host translation. We postulate that the rapid shut-off of host translation in mammalian cells infected with the mosquito-derived virus acts to counter the IFN-β-stimulated transcriptional response.

Common Analysis of Direct RNA SequencinG CUrrently Leads to Misidentification of 5-Methylcytosine Modifications at GCU Motifs

RNA modifications, such as méthylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m5C) modifications is Tombo, which uses an "Alternative Model" to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa including virus, bacteria, fungi, and animals. The algorithm consistently identified a 5-methylcytosine at the central position of a GCU motif. However, it also identified a 5-methylcytosine in the same motif in fully unmodified in vitro transcribed RNA, suggesting that this a frequent false prediction. In the absence of further validation, several published predictions of 5-methylcytosine in human coronavirus and human cerebral organoid RNA in a GCU context should be reconsidered.

Interactions between capsid and viral RNA regulate Chikungunya virus translation in a host-specific manner

Alphaviruses are positive sense, RNA viruses commonly transmitted by an arthropod vector to a mammalian or avian host. In recent years, a number of the Alphavirus members have reemerged as public health concerns. Transmission from mosquito vector to vertebrate hosts requires an understanding of the interaction between the virus and both vertebrate and insect hosts to develop rational intervention strategies. The current study uncovers a novel role for capsid protein during Chikungunya virus replication whereby the interaction with viral RNA in the E1 coding region regulates protein synthesis processes early in infection. Studies done in both the mammalian and mosquito cells indicate that interactions between viral RNA and capsid protein have functional consequences that are host species specific. Our data support a vertebrate-specific role for capsid:vRNA interaction in temporally regulating viral translation in a manner dependent on the PI3K-AKT-mTOR pathway.

Evidence of Adaptive Evolution in Wolbachia-Regulated Gene DNMT2 and Its Role in the Dipteran Immune Response and Pathogen Blocking

Eukaryotic nucleic acid methyltransferase (MTase) proteins are essential mediators of epigenetic and epitranscriptomic regulation. DNMT2 belongs to a large, conserved family of DNA MTases found in many organisms, including holometabolous insects such as fruit flies and mosquitoes, where it is the lone MTase. Interestingly, despite its nomenclature, DNMT2 is not a DNA MTase, but instead targets and methylates RNA species. A growing body of literature suggests that DNMT2 mediates the host immune response against a wide range of pathogens, including RNA viruses. Curiously, although DNMT2 is antiviral in Drosophila, its expression promotes virus replication in mosquito species. We, therefore, sought to understand the divergent regulation, function, and evolution of these orthologs. We describe the role of the Drosophila-specific host protein IPOD in regulating the expression and function of fruit fly DNMT2. Heterologous expression of these orthologs suggests that DNMT2's role as an antiviral is host-dependent, indicating a requirement for additional host-specific factors. Finally, we identify and describe potential evidence of positive selection at different times throughout DNMT2 evolution within dipteran insects. We identify specific codons within each ortholog that are under positive selection and find that they are restricted to four distinct protein domains, which likely influence substrate binding, target recognition, and adaptation of unique intermolecular interactions. Collectively, our findings highlight the evolution of DNMT2 in Dipteran insects and point to structural, regulatory, and functional differences between mosquito and fruit fly homologs.

The oncometabolite L-2-hydroxyglutarate is a common product of dipteran larval development

The oncometabolite L-2-hydroxyglutarate (L-2HG) is considered an abnormal product of central carbon metabolism that is capable of disrupting chromatin architecture, mitochondrial metabolism, and cellular differentiation. Under most circumstances, mammalian tissues readily dispose of this compound, as aberrant L-2HG accumulation induces neurometabolic disorders and promotes renal cell carcinomas. Intriguingly, Drosophila melanogaster larvae were recently found to accumulate high L-2HG levels under normal growth conditions, raising the possibility that L-2HG plays a unique role in insect metabolism. Here we explore this hypothesis by analyzing L-2HG levels in 18 insect species. While L-2HG was present at low-to-moderate levels in most of these species (<100 pmol/mg; comparable to mouse liver), dipteran larvae exhibited a tendency to accumulate high L-2HG concentrations (>100 pmol/mg), with the mosquito Aedes aegypti, the blow fly Phormia regina, and three representative Drosophila species harboring concentrations that exceed 1 nmol/mg - levels comparable to those measured in mutant mice that are unable to degrade L-2HG. Overall, our findings suggest that one of the largest groups of animals on earth commonly generate high concentrations of an oncometabolite during juvenile growth, hint at a role for L-2HG in the evolution of dipteran development, and raise the possibility that L-2HG metabolism could be targeted to restrict the growth of key disease vectors and agricultural pests.

Viral RNA is a target for Wolbachia-mediated pathogen blocking

The ability of the endosymbiont Wolbachia pipientis to restrict RNA viruses is presently being leveraged to curb global transmission of arbovirus-induced diseases. Past studies have shown that virus replication is limited early in arthropod cells colonized by the bacterium, although it is unclear if this phenomenon is replicated in mosquito cells that first encounter viruses obtained through a vertebrate blood meal. Furthermore, these cellular events neither explain how Wolbachia limits dissemination of viruses between mosquito tissues, nor how it prevents transmission of infectious viruses from mosquitoes to vertebrate host. In this study, we try to address these issues using an array of mosquito cell culture models, with an additional goal being to identify a common viral target for pathogen blocking. Our results establish the viral RNA as a cellular target for Wolbachia-mediated inhibition, with the incoming viral RNA experiencing rapid turnover following internalization in cells. This early block in replication in mosquito cells initially infected by the virus thus consequently reduces the production of progeny viruses from these same cells. However, this is not the only contributor to pathogen blocking. We show that the presence of Wolbachia reduces the per-particle infectivity of progeny viruses on naïve mosquito and vertebrate cells, consequently limiting virus dissemination and transmission, respectively. Importantly, we demonstrate that this aspect of pathogen blocking is independent of any particular Wolbachia-host association and affects viruses belonging to Togaviridae and Flaviviridae families of RNA viruses. Finally, consistent with the idea of the viral RNA as a target, we find that the encapsidated virion RNA is less infectious for viruses produced from Wolbachia-colonized cells. Collectively, our findings present a common mechanism of pathogen blocking in mosquitoes that establish a link between virus inhibition in the cell to virus dissemination and transmission.

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

BACKGROUND

Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.

RESULTS

Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.

CONCLUSIONS

Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants

Alphaviruses are arthropod-borne viruses that represent a significant threat to public health at a global level. While the formation of alphaviral nucleocapsid cores, consisting of cargo nucleic acid and the viral capsid protein, is an essential molecular process of infection, the precise interactions between the two partners are ill-defined. A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. Mutational analyses of the cytoplasmic viral RNA-capsid interaction sites revealed a functional role for capsid binding early in infection. Interaction site mutants exhibited decreased viral growth kinetics; however, this defect was not a function of decreased particle production. Rather mutation of the cytoplasmic capsid-RNA interaction sites negatively affected the functional capacity of the incoming viral genomic RNAs leading to decreased infectivity. Furthermore, cytoplasmic capsid interaction site mutants are attenuated in a murine model of neurotropic alphavirus infection. Collectively, the findings of this study indicate that the identified cytoplasmic interactions of the viral capsid protein and genomic RNA, while not essential for particle formation, are necessary for genomic RNA function early during infection. This previously unappreciated role of capsid protein during the alphaviral replication cycle also constitutes a novel virulence determinant.

Alphaviruses can cause significant disease in infected individuals; however, our understanding of the molecular interactions that enable infection and contribute to the development of disease is limited. The work detailed in this manuscript characterizes the interaction of a viral RNA-binding protein, Capsid, with the viral genomic RNA. Importantly, these interactions were found to be at specific sites on the genome but not essential for virus assembly. Mutation of the capsid / RNA interaction sites decreased the replication of the virus and the severity of disease in a mouse model of infection. Taken together, these findings identify a previously undiscovered determinant of disease severity, and provide a potential basis for the development of new vaccines.

Wolbachia elevates host methyltransferase expression to block an RNA virus early during infection

Wolbachia pipientis is an intracellular endosymbiont known to confer host resistance against RNA viruses in insects. However, the causal mechanism underlying this antiviral defense remains poorly understood. To this end, we have established a robust arthropod model system to study the tripartite interaction involving Sindbis virus and Wolbachia strain wMel within its native host, Drosophila melanogaster. By leveraging the power of Drosophila genetics and a parallel, highly tractable D. melanogaster derived JW18 cell culture system, we determined that in addition to reducing infectious virus production, Wolbachia negatively influences Sindbis virus particle infectivity. This is further accompanied by reductions in viral transcript and protein levels. Interestingly, unchanged ratio of proteins to viral RNA copies suggest that Wolbachia likely does not influence the translational efficiency of viral transcripts. Additionally, expression analyses of candidate host genes revealed D. melanogaster methyltransferase gene Mt2 as an induced host factor in the presence of Wolbachia. Further characterization of viral resistance in Wolbachia-infected flies lacking functional Mt2 revealed partial recovery of virus titer relative to wild-type, accompanied by complete restoration of viral RNA and protein levels, suggesting that Mt2 acts at the stage of viral genome replication. Finally, knockdown of Mt2 in Wolbachia uninfected JW18 cells resulted in increased virus infectivity, thus demonstrating its previously unknown role as an antiviral factor against Sindbis virus. In conclusion, our findings provide evidence supporting the role of Wolbachia-modulated host factors towards RNA virus resistance in arthropods, alongside establishing Mt2's novel antiviral function against Sindbis virus in D. melanogaster.

Alphavirus RNA synthesis and non-structural protein functions

The members of the genus Alphavirus are positive-sense RNA viruses, which are predominantly transmitted to vertebrates by a mosquito vector. Alphavirus disease in humans can be severely debilitating, and depending on the particular viral species, infection may result in encephalitis and possibly death. In recent years, alphaviruses have received significant attention from public health authorities as a consequence of the dramatic emergence of chikungunya virus in the Indian Ocean islands and the Caribbean. Currently, no safe, approved or effective vaccine or antiviral intervention exists for human alphavirus infection. The molecular biology of alphavirus RNA synthesis has been well studied in a few species of the genus and represents a general target for antiviral drug development. This review describes what is currently understood about the regulation of alphavirus RNA synthesis, the roles of the viral non-structural proteins in this process and the functions of cis-acting RNA elements in replication, and points to open questions within the field.

Insect antiviral innate immunity: pathways, effectors, and connections

Insects are infected by a wide array of viruses some of which are insect restricted and pathogenic, and some of which are transmitted by biting insects to vertebrates. The medical and economic importance of these viruses heightens the need to understand the interaction between the infecting pathogen and the insect immune system in order to develop transmission interventions. The interaction of the virus with the insect host innate immune system plays a critical role in the outcome of infection. The major mechanism of antiviral defense is the small, interfering RNA pathway that responds through the detection of virus-derived double-stranded RNA to suppress virus replication. However, other innate antimicrobial pathways such as Imd, Toll, and Jak-STAT and the autophagy pathway have also been shown to play important roles in antiviral immunity. In this review, we provide an overview of the current understanding of the main insect antiviral pathways and examine recent findings that further our understanding of the roles of these pathways in facilitating a systemic and specific response to infecting viruses.

Role for subgenomic mRNA in host translation inhibition during Sindbis virus infection of mammalian cells

Sindbis virus subgenomic mRNA is efficiently translated in infected vertebrate cells whereas host translation is shut-off. Deletions in the 5'UTR of the subgenomic mRNA were made to investigate its role in viral gene expression. Deletion of nucleotides 1-10 and 11-20 caused a small plaque phenotype, reduced levels of subgenomic mRNA and structural proteins, and increased expression of nonstructural proteins. Whereas deletion 1-10 virus inhibited cellular protein synthesis, deletion 11-20 did so inefficiently. A large plaque revertant of deletion 11-20, possessing a duplication of the subgenomic promoter region, produced subgenomic mRNA at WT levels and restored inhibition of host protein synthesis. Further analysis of the mutant and revertant 5'UTR sequences showed the ability to shut-off host cell translation correlated with the efficiency of translation of subgenomic mRNA. We propose that the translational efficiency and quantity of the subgenomic mRNA play a role in inhibition of host cell translation.

Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra

Searching spectral libraries in MS/MS is an important new approach to improving the quality of peptide and protein identification. The idea relies on the observation that ion intensities in an MS/MS spectrum of a given peptide are generally reproducible across experiments, and thus, matching between spectra from an experiment and the spectra of previously identified peptides stored in a spectral library can lead to better peptide identification compared to the traditional database search. However, the use of libraries is greatly limited by their coverage of peptide sequences: even for well-studied organisms a large fraction of peptides have not been previously identified. To address this issue, we propose to expand spectral libraries by predicting the MS/MS spectra of peptides based on the spectra of peptides with similar sequences. We first demonstrate that the intensity patterns of dominant fragment ions between similar peptides tend to be similar. In accordance with this observation, we develop a neighbor-based approach that first selects peptides that are likely to have spectra similar to the target peptide and then combines their spectra using a weighted K-nearest neighbor method to accurately predict fragment ion intensities corresponding to the target peptide. This approach has the potential to predict spectra for every peptide in the proteome. When rigorous quality criteria are applied, we estimate that the method increases the coverage of spectral libraries available from the National Institute of Standards and Technology by 20-60%, although the values vary with peptide length and charge state. We find that the overall best search performance is achieved when spectral libraries are supplemented by the high quality predicted spectra.

Sindbis virus infectivity improves during the course of infection in both mammalian and mosquito cells

Alphaviruses are enveloped, single-stranded positive sense RNA viruses that are transmitted by an arthropod vector to a wide host range, including avian and mammalian species. Arthropods and vertebrates have different cellular environments and this may cause the different cellular pathologies that are observed between the invertebrate vector and vertebrate hosts in both whole organisms and cultured cell lines. In this report, we used Sindbis virus and examined mosquito and mammalian cell lines for their ability to produce progeny virus particles. Total particles produced, viral titers, and overall infectivity (or the ratio of total particles-to-infectious particles) was investigated. Our results show (1) Sindbis infectivity is more a function of the host cell used in titering the virus rather than the cell line used to produce the virus, (2) the number of total and infectious particles produced is cell line dependent, and (3) the infectivity of released virus particles improves during the course of infection in both cells that have cytolytic infections and persistent infections.

Natural resistance-associated macrophage protein is a cellular receptor for sindbis virus in both insect and mammalian hosts

Alphaviruses, including several emerging human pathogens, are a large family of mosquito-borne viruses with Sindbis virus being a prototypical member of the genus. The host factor requirements and receptors for entry of this class of viruses remain obscure. Using a Drosophila system, we identified the divalent metal ion transporter natural resistance-associated macrophage protein (NRAMP) as a host cell surface molecule required for Sindbis virus binding and entry into Drosophila cells. Consequently, flies mutant for dNRAMP were protected from virus infection. NRAMP2, the ubiquitously expressed vertebrate homolog, mediated binding and infection of Sindbis virus into mammalian cells, and murine cells deficient for NRAMP2 were nonpermissive to infection. Alphavirus glycoprotein chimeras demonstrated that the requirement for NRAMP2 is at the level of Sindbis virus entry. Given the conserved structure of alphavirus glycoproteins, and the widespread use of transporters for viral entry, other alphaviruses may use conserved multipass membrane proteins for infection.

Immunohistochemistry in the evaluation of neovascularization in tumor xenografts

Angiogenesis, or neovascularization, is known to play an important role in the neoplastic progression leading to metastasis. CD31 or Factor VIII-related antigen (F VIII RAg) immunohistochemistry is widely used in experimental studies for quantifying tumor neovascularization in immunocompromised animal models implanted with transformed human cell lines. Quantification, however, can be affected by variations in the methodology used to measure vascularization including antibody selection, antigen retrieval (AR) pretreatment, and evaluation techniques. To examine this further, we investigated the microvessel density (MVD) and the intensity of microvascular staining among five different human tumor xenografts and a mouse syngeneic tumor using anti-CD31 and F VIII RAg immunohistochemical staining. Different AR methods also were evaluated. Maximal retrieval of CD31 was achieved using 0.5 M Tris (pH 10) buffer, while maximum retrieval of F VIII RAg was achieved using 0.05% pepsin treatment of tissue sections. For each optimized retrieval condition, anti-CD31 highlighted small vessels better than F VIII RAg. Furthermore, the MVD of CD31 was significantly greater than that of F VIII RAg decorated vessels (p<0.001). The choice of antibody and AR method has a significant affect on immunohistochemical findings when studying angiogenesis. One also must use caution when comparing studies in the literature that use different techniques and reagents.

Characterization of purified Sindbis virus nsP4 RNA-dependent RNA polymerase activity in vitro

The Sindbis virus RNA-dependent RNA polymerase (nsP4) is responsible for the replication of the viral RNA genome. In infected cells, nsP4 is localized in a replication complex along with the other viral non-structural proteins. nsP4 has been difficult to homogenously purify from infected cells due to its interactions with the other replication proteins and the fact that its N-terminal residue, a tyrosine, causes the protein to be rapidly turned over in cells. We report the successful expression and purification of Sindbis nsP4 in a bacterial system, in which nsP4 is expressed as an N-terminal SUMO fusion protein. After purification the SUMO tag is removed, resulting in the isolation of full-length nsP4 possessing the authentic N-terminal tyrosine. This purified enzyme is able to produce minus-strand RNA de novo from plus-strand templates, as well as terminally add adenosine residues to the 3' end of an RNA substrate. In the presence of the partially processed viral replicase polyprotein, P123, purified nsP4 is able to synthesize discrete template length minus-strand RNA products. Mutations in the 3' CSE or poly(A) tail of viral template RNA prevent RNA synthesis by the replicase complex containing purified nsP4, consistent with previously reported template requirements for minus-strand RNA synthesis. Optimal reaction conditions were determined by investigating the effects of time, pH, and the concentrations of nsP4, P123 and magnesium on the synthesis of RNA.

Expression of the oligopeptide transporter, PepT1, in larval Atlantic cod (Gadus morhua)

The intestinal absorption of di- and tri-peptides generally occurs via the oligopeptide transporter, PepT1. This study evaluates the expression of PepT1 in larval Atlantic cod (Gadus morhua) during the three weeks following the onset of exogenous feeding. Larval Atlantic cod were fed either wild captured zooplankton or enriched rotifers. cDNA was prepared from whole cod larvae preceding first feeding and at 1000 each Tuesday and Thursday for the following three weeks. Spatial and temporal expression patterns of PepT1 mRNA were compared between fish consuming the two prey types using in situ hybridization and quantitative real-time PCR. Results indicated that PepT1 mRNA was expressed prior to the onset of exogenous feeding. In addition, PepT1 was expressed throughout the digestive system except the esophagus and sphincter regions. Expression slightly increased following first-feeding and continued to increase throughout the study for larvae feeding on both prey types. When comparing PepT1 expression in larvae larger than 0.15-mg dry mass with expression levels in larvae prior to feeding, no differences were detected for larvae fed rotifers, but the larvae fed zooplankton had significantly greater PepT1 expression at the larger size. In addition, PepT1 expression in the zooplankton fed larvae larger than 0.15-mg dry mass had significantly greater expression than rotifer fed larvae of a similar weight. Switching prey types did not affect PepT1 expression. These results indicate that Atlantic cod PepT1 expression was slightly different relative to dietary treatment during the three weeks following first-feeding. In addition, PepT1 may play an important role in the larval nutrition since it is widely expressed in the digestive tract.

The aetiology of spinal deformity in Atlantic salmon, Salmo salar L.: influence of different commercial diets on the incidence and severity of the preclinical condition in salmon parr under two contrasting husbandry regimes

A large-scale trial of the effect of different commercial diets on the incidence of preclinical spinal deformation, as assessed by radiography, and the influence of two contrasting rearing systems was carried out. Two sets of three populations of Atlantic salmon, each of 20 000 first feeding fry of identical hatchery origin, created from equal numbers of eggs from 15 different families, were reared under commercial conditions on two different farms. Three commercial (closed formula) extruded fish meal-based diets were used in this study (diets A, B & C). Each diet was fed to one population of 20 000 fish at each site. Fish were fed a percentage of their body weight per day, with feeding rates set at commercial levels, based on water temperature, day length and fish biomass. Additional hand feeding was used to ensure satiation in all tanks. Fish in each tank were bulk-weighed and counted at the beginning and at 2-week intervals throughout the study. The fish were grown for 30 weeks. In addition, phosphorus (P) digestibility was evaluated by in-feed absorption testing in rainbow trout. The morphology of the radiographic lesions conformed to those described previously. Statistical analysis using multivariate regression analysis showed that date of sampling, site and diet were all statistically significant (P < 0.001) on univariable analysis. Farm A had significantly more affected fish than farm B (P < 0.001), which may have been attributable to variation in dissolved oxygen levels. The available dietary P levels were low in each diet. The number of fish affected in the group of fish being fed diet B was significantly lower than in the groups being fed diets A or C (P < 0.001). It appears most likely that the occurrence of preclinical radiographically apparent defects in parr which are believed to lead to the condition known as 'spinal deformity' is predominantly caused by a deficiency of available dietary P in first-feeding fry. The availability of dietary P may also vary considerably between diets formulated using different ingredients. Phytate-P associated with plant ingredients may affect the availability of P as well as other essential dietary nutrients. Additionally, diets for the production of salmonids in fresh water are currently formulated to keep P effluent to a minimum compatible with healthy spinal development. These various factors combine to make it crucial that small Atlantic salmon, especially first-feeding fry, are provided with carefully formulated diets fortified to an adequate level with a high quality source of available P.

Structural and functional analyses of stem-loop 1 of the Sindbis virus genome

Alphavirus genome function is controlled by elements at both the 5' and 3' ends. The 5' 220 nt of the Sindbis virus genome is predicted to consist of four stem-loop structures the first of which has been demonstrated to be required for efficient minus-strand RNA synthesis. To understand the role of the structure of the first stem-loop (SL1) in regulating genome function, we performed enzymatic and chemical probing analyses. There were significant differences between the computer-predicted structures and our experimental data. In the 5' terminus, two loop regions appear to be interacting in a complex and interdependent fashion with non-Watson-Crick interactions involving multiple adenosine residues playing a critical role in determining the overall structure. Some of the mutations that disrupted these interactions had significant affects, both positive and negative, on minus-strand synthesis, and translational efficiency was generally increased. In the context of full-length virus, these structural changes resulted in reduced virus growth kinetics particularly in mosquito cells suggesting host-specific effects of mutations in this region of the viral genome. Possible SL1 structures based on our experimental data are discussed.

Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers

Nucleic acid aptamers can potentially be developed as broad-spectrum antiviral agents. Single-stranded DNA (ssDNA) aptamer RT1t49 inhibits reverse transcriptases (RT) from HIV-1 and diverse lentiviral subtypes with low nanomolar values of Kd and IC₅₀. To dissect the structural requirements for inhibition, RT-catalyzed DNA polymerization was measured in the presence of RT1t49 variants. Three structural domains were found to be essential for RT inhibition by RT1t49: a 5′ stem (stem I), a connector and a 3′ stem (stem II) capable of forming multiple secondary structures. Stem I tolerates considerable sequence plasticity, suggesting that it is recognized by RT more by structure than by sequence-specific contacts. Truncating five nucleotides from the 3′ end prevents formation of the most stable stem II structure, yet has little effect on IC50 across diverse HIV-1, HIV-2 and SIV_CPZ RT. When bound to wild-type RT or an RNase H active site mutant, site-specifically generated hydroxyl radicals cleave after nucleotide A32. Cleavage is eliminated by either of two polymerase (pol)-active site mutants, strongly suggesting that A32 lies within the RT pol-active site. These data suggest a model of ssDNA aptamer–RT interactions and provide an improved molecular understanding of a potent, broad-spectrum ssDNA aptamer.

Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA

Alphaviruses are a group of arthropod-borne human and animal pathogens that can cause epidemics of significant public health and economic consequence. Alphavirus RNA synthesis requires four virally encoded nonstructural proteins and probably a number of cellular proteins. Using comparative two-dimensional electrophoresis we were able to identify proteins enriched in cytoplasmic membrane fractions containing viral RNA synthetic complexes following infection with Sindbis virus. Our studies demonstrated the following: (i) the host protein hnRNP K is enriched in cytoplasmic membrane fractions following Sindbis virus infection, (ii) viral nonstructural proteins co-immunoprecipitate with hnRNP K, (iii) nsP2 and hnRNP K co-localize in the cytoplasm of Sindbis virus infected cells, (iv) Sindbis virus subgenomic mRNA, but not genomic RNA co-immunoprecipitates with hnRNP K, (v) viral RNA does not appear to be required for the interaction of hnRNP K with the nonstructural proteins. Potential functions of hnRNP K during virus replication are discussed.

Breast cancer metastasis to bone: evaluation of bioluminescent imaging and microSPECT/CT for detecting bone metastasis in immunodeficient mice

This study sought to determine if weekly X-ray exposure affected breast cancer cell metastasis to bone and to also evaluate the use of bioluminescent imaging (BLI) and microSPECT for detection of metastatic bone lesions. Five week old nude mice were randomly assigned to the CT exposed (n = 7) and no CT exposure (n = 6) treatment groups. Mice received an intracardiac injection of MDA-MB-435 human breast cancer cells transduced with luciferase, or a sham injection (saline). The CT exposed group of mice received CT irradiation once a week for 5 weeks. All mice underwent weekly BLI and select mice received Tc-99m-MDP followed by microSPECT imaging after 5 weeks. Pathological evaluation and histomorphometry were used to assess the affect of CT X-rays on bone metastasis and to evaluate BLI. BLI results found no significant difference in metastasis between animals that received CT and those that did not (P > 0.05); however, histomorphometry of the knee joints revealed a significant increase (P = 0.029) in tumor area of the leg bones in mice that received CT exposure (60% +/- 7%) compared to animals that did not receive CT scans (33% +/- 8%). Compared to histological analysis, BLI of the leg and spine was determined to have excellent sensitivity (100%), good specificity (80-90%) and accuracy (90-96%), a positive predictive value of 81-93% and a 100% negative predictive value. Thus, multi-modality imaging techniques can be very useful for monitoring bone metastasis, however microCT X-rays should be used judiciously in order to limit irradiation that may stimulate increased metastasis to specific regions of the skeleton. MicroSPECT imaging did not detect metastatic lesions in the legs of these young nude mice.

Single-stranded DNA aptamer RT1t49 inhibits RT polymerase and RNase H functions of HIV type 1, HIV type 2, and SIVCPZ RTs

Natural and selected resistance of HIV-1 to current anti-HIV drugs continues to pose serious problems to the development of HIV-1 antivirals. The viral reverse transcriptase (RT) is a proven therapeutic target. Single-stranded RNA and DNA (ssRNA and ssDNA) aptamers have been selected that specifically and potently inhibit RT function. In particular, the ssDNA aptamer RT1t49 was previously selected to recognize the RT from a subtype B strain of HIV-1 and binds with a reported K(d) of 4 nM. In the present work, we show that RT1t49 inhibits recombinant RT cloned from diverse branches of the primate lentiviral family. Aptamer concentrations required for half-maximal inhibition of all HIV-1, HIV-2, and SIV(CPZ) RTs assayed were in the low-to mid-nanomolar range for both polymerase and RNase H activities. Using pre-steady-state and order-of-addition kinetic analyses, we also established that this ssDNA aptamer competes with primer-template for access to RT, and that addition of a nucleoside analog RT inhibitor (NRTI) to the in vitro reaction enhanced the overall effectiveness of both drugs, while nonnucleoside analog RT inhibitors (NNRTIs) exhibited simple additivity. This is the first demonstration of universal inhibition of HIV and SIV(cpz) RTs by a nucleic acid aptamer and supports previous reports suggesting that resistance to RT1t49 may be exceptionally infrequent.

Cross-clade inhibition of recombinant human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus SIVcpz reverse transcriptases by RNA pseudoknot aptamers

Reverse transcriptase (RT) remains a primary target in therapies directed at human immunodeficiency virus type 1 (HIV-1). RNA aptamers that bind RT from HIV-1 subtype B have been shown to protect human cells from infection and to reduce viral infectivity, but little is known about the sensitivity of the inhibition to amino sequence variations of the RT target. Therefore, we assembled a panel of 10 recombinant RTs from phylogenetically diverse lentiviral isolates (including strains of HIV-1, simian immunodeficiency virus SIVcpz, and HIV-2). After validating the panel by measuring enzymatic activities and inhibition by small-molecule drugs, dose-response curves for each enzyme were established for four pseudoknot RNA aptamers representing two structural subfamilies. All four aptamers potently inhibited RTs from multiple HIV-1 subtypes. For aptamers carrying family 1 pseudoknots, natural resistance was essentially all-or-none and correlated with the identity of the amino acid at position 277. In contrast, natural resistance to aptamers carrying the family 2 pseudoknots was much more heterogeneous, both in degree (gradation of 50% inhibitory concentrations) and in distribution across clades. Site-directed and subunit-specific mutagenesis identified a common R/K polymorphism within the p66 subunit as a primary determinant of resistance to family 1, but not family 2, pseudoknot aptamers. RNA structural diversity therefore translates into a nonoverlapping spectrum of mutations that confer resistance, likely due to differences in atomic-level contacts with RT.

Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity

The RNA-dependent RNA polymerase nsP4 is an integral part of the alphavirus replication complex. To define the role of nsP4 in viral RNA replication and for a structure-function analysis, we expressed Sindbis virus nsP4 in Escherichia coli. The core catalytic domain of nsP4 (Delta97nsP4, a deletion of the N-terminal 97 amino acids), which consists of the predicted polymerase domain containing the GDD amino acid motif required for viral RNA synthesis, was stable against proteolytic degradation during expression. Therefore, the recombinant core domain and selected mutants were expressed and purified to homogeneity. We determined that Delta97nsP4 possesses terminal adenylyltransferase (TATase) activity, as it specifically catalyzed the addition of adenine to the 3' end of an acceptor RNA in the presence of divalent cations. Furthermore, Delta97nsP4 is unable to transfer other nucleotides (UTP, CTP, GTP, and dATP) to the acceptor RNA in the absence or presence of other nucleotides. Delta97nsP4 possessing a GDD-to-GAA mutation completely inactivates the enzymatic activity. However, a GDD-to-SNN mutation did not inactivate the enzyme but reduced its activity to approximately 45% of that of the wild type in the presence of Mg(2+). Investigation of the TATase of the GDD-to-SNN mutant revealed that it had TATase equivalent to that of the wild type in the presence of Mn(2+). Identification of Delta97nsP4 TATase activity suggests a novel function of the alphavirus RNA-dependent RNA polymerase in the maintenance and repair of the poly(A) tail, an element required for replication of the viral genome.

Template requirements for recognition and copying by Sindbis virus RNA-dependent RNA polymerase

The Sindbis virus (SIN) nonstructural protein nsP4 possesses the RNA-dependent RNA polymerase activity required for the replication of the SIN genome and transcription of a subgenomic mRNA during infection. Isolation of this protein from other viral components of the RNA synthetic complex allowed the characterization of template requirements for nsP4-mediated genome replication. The major findings of this study are: (i) in the absence of other viral proteins nsP4 is capable of copying SIN plus- and minus-strand templates, but does not transcribe subgenomic RNA; (ii) mutations in the 3' conserved sequence element and poly(A) tail of the plus-strand template prevent nsP4-mediated de novo initiation of minus-strand RNA synthesis; (iii) nsP4-dependent terminal addition of nucleotides occurs on template RNA possessing certain mutations in the 3'CSE and polyadenylate tail ; (iv) nsP4 is capable of minus-strand synthesis independent of the sequence at the 5' end of the template; (v) an A-U rich sequence in the 3'CSE represents a binding site for a replicase component, probably nsP4; (vi) plus-strand genomic RNA synthesis is dependent on the 3' end of the minus-strand template. These studies begin to define the specific interactions with the viral RNA templates mediated by individual components of the viral replication complex and suggest a model for ternary complex formation during the initiation of minus-strand RNA synthesis.

The role of the 3' terminus of the Sindbis virus genome in minus-strand initiation site selection

Genome replication of plus-strand RNA viruses begins with the generation of a minus-strand copy of the genome. Minus-strand synthesis must initiate at or close to the 3' end of the genome and progress to processive elongation to yield the appropriate template for genomic RNA synthesis. The Sindbis virus genome possesses a 3' polyadenylate tail preceded by a 19 nucleotide conserved sequence element (3' CSE). Analyses of in vitro and in vivo synthesized minus-strand RNA presented in this manuscript identify the cytidylate residue immediately preceding the poly (A) tail as the predominant wild-type initiation site. Mutations in the poly (A) tail and the 3' CSE caused the initiation site to shift to the poly (A) tail. Analysis of the products of non-wild-type initiation events demonstrated that they are not productively elongated. This study indicates that full-length minus-strand RNA synthesis is dependent upon initiation occurring at the appropriate site and suggests a mechanism for selection and maintenance of the wt 3' CSE and poly (A) tail.

Requirements at the 3' end of the sindbis virus genome for efficient synthesis of minus-strand RNA

The 3'-untranslated region of the Sindbis virus genome is 0.3 kb in length with a 19-nucleotide conserved sequence element (3' CSE) immediately preceding the 3'-poly(A) tail. The 3' CSE and poly(A) tail have been assumed to constitute the core promoter for minus-strand RNA synthesis during genome replication; however, their involvement in this process has not been formally demonstrated. Utilizing both in vitro and in vivo analyses, we have examined the role of these elements in the initiation of minus-strand RNA synthesis. The major findings of this study with regard to efficient minus-strand RNA synthesis are the following: (i) the wild-type 3' CSE and the poly(A) tail are required, (ii) the poly(A) tail must be a minimum of 11 to 12 residues in length and immediately follow the 3' CSE, (iii) deletion or substitution of the 3' 13 nucleotides of the 3' CSE severely inhibits minus-strand RNA synthesis, (iv) templates possessing non-wild-type 3' sequences previously demonstrated to support virus replication do not program efficient RNA synthesis, and (v) insertion of uridylate residues between the poly(A) tail and a non-wild-type 3' sequence can restore promoter function to a limited extent. This study shows that the optimal structure of the 3' component of the minus-strand promoter is the wild-type 3' CSE followed a poly(A) tail of at least 11 residues. Our findings also show that insertion of nontemplated bases can restore function to an inactive promoter.

Protein and lipid sources affect cholesterol concentrations of juvenile Pacific white shrimp, Litopenaeus vannamei (Boone)

Two experiments were conducted to evaluate the effects of protein and lipid sources on cholesterol, AA, and fatty acid content, and on biological performance of juvenile Pacific white shrimp, Litopenaeus vannamei (Boone). In Exp. 1, seven isonitrogenous and isocaloric diets were prepared using fish meal; soybean meal; casein; fish meal + soybean meal; fish meal + casein; soybean meal + casein; and fish meal + soybean meal + casein. In Exp. 2, seven isonitrogenous and isocaloric diets were prepared using fish oil; soy oil; poultry fat; fish oil + soy oil; fish oil + poultry fat; soy oil + poultry fat; and fish oil + soy oil + poultry fat. Nine shrimp (average BW 570 mg) were stocked per 60-L tank, with three tanks per diet in each experiment. Shrimp were fed to apparent satiation twice daily for 28 d. Protein sources affected shrimp cholesterol, feed consumption, feed efficiency, protein consumption, protein efficiency ratio, and crude body fat (P < or = 0.05), but not weight gain, survival, hepatosomatic index, body protein, ash, and AA composition. Body (without hepatopancreas) cholesterol concentrations were the highest in shrimp fed the diet containing fish meal (0.81%), lowest for those fed the casein diet (0.64%), and intermediate in the other dietary treatment groups (range 0.71 to 0.74%). Lipid source also affected shrimp body cholesterol, body fatty acid profiles, and fatty acid profiles in the hepatopancreas (P < or = 0.05), but not growth performance, body protein, fat, ash, and cholesterol concentrations in the hepatopancreas. Shrimp fed the fish oil diet had the highest body cholesterol (0.75%), whereas those fed the soy oil or poultry fat diets were lowest (0.66 and 0.65%, respectively). Results indicate that by replacing fish meal and fish oil with soybean meal and soy oil, shrimp growth performance is not affected, but body cholesterol concentration is reduced.

The pathology of phosphorus deficiency in fish--a review

Phosphorus (P) is an essential component of fish diets. Its deficiency affects not only hard tissues, where it is responsible for rickets, leading to skeletal malformation, but also influences various aspects of intermediary metabolism, and thus growth and feed conversion. Therefore, optimizing the dietary inclusion level is critical at all times. As the aquaculture industry has expanded, so the effects of P in farm effluents, derived from metabolic and uneaten food sources, have also become recognized. Diets are increasingly formulated on a basis that will not only provide adequate P for fish needs, but also endeavour to ensure minimal acceptable P levels in effluents at the same time. Many variables influence P requirements and P availability in fish diets, so it is inadvisable to feed diets formulated to an assumed minimum dietary requirement level, irrespective of the advantages that such a formulation may provide to environmental impact.

Hepatitis C virus RNA synthesis in a cell-free system isolated from replicon-containing hepatoma cells

A number of hepatitis C virus (HCV) proteins, including NS5B, the RNA-dependent RNA polymerase, were detected in membrane fractions from Huh7 cells containing autonomously replicating HCV RNA replicons. These membrane fractions were used in a cell-free system for the analysis of HCV RNA replication. Initial characterization revealed a reaction in which the production of replicon RNA increased over time at temperatures ranging from 25 to 40 degrees C. Heparin sensitivity and nucleotide starvation experiments suggested that de novo initiation was occurring in this system. Both Mn2+ and Mg2+ cations could be used in the reaction; however, concentrations of Mn2+ greater than 1 mM were inhibitory. Compounds shown to inhibit recombinant NS3 and NS5B activity in vitro were found to inhibit RNA synthesis in the cell-free system. This system should be useful for biochemical analysis of HCV RNA synthesis by a multisubunit membrane-associated replicase and for evaluating potential antiviral agents identified in biochemical or cell-based screens.

DrosophilaAmphiphysin is implicated in protein localization and membrane morphogenesis but not in synaptic vesicle endocytosis

Amphiphysin family members are implicated in synaptic vesicle endocytosis, actin localization and one isoform is an autoantigen in neurological autoimmune disorder; however, there has been no genetic analysis of Amphiphysin function in higher eukaryotes. We show that Drosophila Amphiphysin is localized to actin-rich membrane domains in many cell types, including apical epithelial membranes, the intricately folded apical rhabdomere membranes of photoreceptor neurons and the postsynaptic density of glutamatergic neuromuscular junctions. Flies that lack all Amphiphysin function are viable, lack any observable endocytic defects, but have abnormal localization of the postsynaptic proteins Discs large, Lethal giant larvae and Scribble, altered synaptic physiology, and behavioral defects. Misexpression of Amphiphysin outside its normal membrane domain in photoreceptor neurons results in striking morphological defects. The strong misexpression phenotype coupled with the mild mutant and lack of phenotypes suggests that Amphiphysin acts redundantly with other proteins to organize specialized membrane domains within a diverse array of cell types.

Soluble guanylate cyclase is required during development for visual system function in Drosophila

A requirement for nitric oxide (NO) in visual system development has been demonstrated in many model systems, but the role of potential downstream effector molecules has not been established. Developing Drosophila photoreceptors express an NO-sensitive soluble guanylate cyclase (sGC), whereas the optic lobe targets express NO synthase. Both of these molecules are expressed after photoreceptor outgrowth to the optic lobe, when retinal growth cones are actively selecting their postsynaptic partners. We have previously shown that inhibition of the NO-cGMP pathway in vitro leads to overgrowth of retinal axons. Here we examined flies mutant for the alpha subunit gene of the Drosophila sGC (Gcalpha1). This mutation severely reduced but did not abolish GCalpha1 protein levels and NO-stimulated sGC activity in the developing photoreceptors. Although few mutant individuals possessed a disorganized retinal projection pattern, pharmacological NOS inhibition during metamorphosis increased this disorganization in mutants to a greater degree than in the wild type. Adult mutants lacked phototactic behavior, and the off-transient component of electroretinograms was frequently absent or greatly reduced in amplitude. Normal phototaxis and off-transient amplitude were restored by heat shock-mediated Gcalpha1 expression applied during metamorphosis but not in the adult. We propose that diminished sGC activity in the visual system during development causes inappropriate or inadequate formation of first-order retinal synapses, leading to defects in visual system function and visually mediated behavior.

Diagnosis and treatment of piriformis syndrome

Piriformis syndrome remains a controversial diagnosis, despite its having first been described over 60 years ago. The controversy stems from several factors: variable and sometimes unclear cause, similarity to other more easily recognizable causes of sciatica, lack of consistent objective diagnostic findings, and relative rarity. Nevertheless, it is reasonable to infer that sciatic pain may be caused by compression anywhere along its length, from the spinal root level to the popliteal fossa, as is peripheral nerve entrapment elsewhere in the body. Pathologic changes at the greater sciatic notch may well be the source of sciatic pain and should be considered by the clinician. The diagnosis of piriformis syndrome remains one of exclusion, however, and in patients who present with sciatica, more common causes such as lumbar disease should be investigated and ruled out first. After excluding the most common causes of sciatica, physicians can use the criteria described here to investigate the possibility of piriformis syndrome. If properly diagnosed, it can often be treated effectively with either surgical or nonsurgical means.

Epidural fibrosis and the failed back surgery syndrome: history and physical findings

Patients who present with recurrent symptoms after surgical intervention aimed at correcting their lumbosacral disease pose a therapeutic challenge. A heterogeneous group of factors may underlie symptom recurrence and formulation of a therapeutic strategy depends on an accurate diagnosis of the patient's underlying problem. In this review, the authors discuss the relevant historical and physical findings in patients with epidural fibrosis and the failed back surgery syndrome.

An unusual multiple drug intoxication case involving citalopram

A 47-year-old male with a history of drug abuse and suicide attempts was found dead at home. The death scene investigation showed evidence of cocaine abuse and multiple drug ingestion. Citralopram, a new selective serotonin reuptake inhibitor, cocaine, oxycodone, promethazine, propoxyphene, and norpropoxyphene were identified and quantitated in the postmortem samples by gas chromatography-mass spectrometry. The concentration of citalopram in the femoral blood was 0.88 mg/L. The heart blood concentration was 1.16 mg/L. Femoral blood concentrations of the other drugs were as follows: cocaine, 0.03 mg/L; oxycodone, 0.06 mg/L; promethazine, 0.02 mg/L; propoxyphene, 0.02 mg/L; and norpropoxyphene, 0.07 mg/L. Other tissue samples were also analyzed. The concentrations of cocaine, oxycodone, promethazine, and propoxyphene in the blood, liver, brain, and gastric contents did not suggest an intentional overdose. However, the possibility of multiple drug interactions including citalopram was evident. In this case, the citalopram concentrations were consistent with those reported in fatal cases involving multiple drug use. Citalopram was present in urine at a concentration of 0.9 mg/L.

A molecular pathway for light-dependent photoreceptor apoptosis in Drosophila

Light-induced photoreceptor apoptosis occurs in many forms of inherited retinal degeneration resulting in blindness in both vertebrates and invertebrates. Though mutations in several photoreceptor signaling proteins have been implicated in triggering this process, the molecular events relating light activation of rhodopsin to photoreceptor death are yet unclear. Here, we uncover a pathway by which activation of rhodopsin in Drosophila mediates apoptosis through a G protein-independent mechanism. This process involves the formation of membrane complexes of phosphorylated, activated rhodopsin and its inhibitory protein arrestin, and subsequent clathrin-dependent endocytosis of these complexes into a cytoplasmic compartment. Together, these data define the proapoptotic molecules in Drosophila photoreceptors and indicate a novel signaling pathway for light-activated rhodopsin molecules in control of photoreceptor viability.

Genetically similar transduction mechanisms for touch and hearing in Drosophila

To test the effects of mechanosensory mutations on hearing in Drosophila, we have recorded sound-evoked potentials originating from ciliated sensory neurons in Johnston's organ, the chordotonal organ that is the sensory element of the fly's antennal ear. Electrodes inserted close to the antennal nerve were used to record extracellular compound potentials evoked by near-field sound stimuli. Sound-evoked potentials are absent in atonal mutant flies, which lack Johnston's organ. Mutations in many genes involved in mechanotransduction by tactile bristles also eliminate or reduce the Johnston's organ response, indicating that related transduction mechanisms operate in each type of mechanosensory organ. In addition, the sound-evoked response is affected by two mutations that do not affect bristle mechanotransduction, beethoven (btv) and touch-insensitive-larvaB (tilB). btv shows defects in the ciliary dilation, an elaboration of the axoneme that is characteristic of chordotonal cilia. tilB, which also causes male sterility, shows structural defects in sperm flagellar axonemes. This suggests that in addition to the shared transduction mechanism, axonemal integrity and possibly ciliary motility are required for signal amplification or transduction by chordotonal sensory neurons.

The Cys(3)-His(1) motif of the respiratory syncytial virus M2-1 protein is essential for protein function

The M2 gene of respiratory syncytial (RS) virus has two open reading frames (ORFs). ORF1 encodes a 22-kDa protein termed M2-1. The M2-1 protein contains a Cys(3)-His(1) motif (C-X(7)-C-X(5)-C-X(3)-H) near the amino terminus. This motif is conserved in all human, bovine, and ovine strains of RS virus. A similar motif found in the mammalian transcription factor Nup475 has been shown to bind zinc. The M2-1 protein of human RS virus functions as a transcription factor which increases polymerase processivity, and it enhances readthrough of intergenic junctions during RS virus transcription, thereby acting as a transcription antiterminator. The M2-1 protein also interacts with the nucleocapsid protein. We examined the effects of mutations of cysteine and histidine residues predicted to coordinate zinc in the Cys(3)-His(1) motif on transcription antitermination and N protein binding. We found that mutating the predicted zinc-coordinating residues, the cysteine residues at amino acid positions 7 and 15 and the histidine residue at position 25, prevented M2-1 from enhancing transcriptional readthrough. In contrast, mutations of amino acids within this motif not predicted to coordinate zinc had no effect. Mutations of the predicted zinc-coordinating residues in the Cys(3)-His(1) motif also prevented M2-1 from interacting with the nucleocapsid protein. One mutation of a noncoordinating residue in the motif which did not affect readthrough during transcription, E10G, prevented interaction with the nucleocapsid protein. This suggests that M2-1 does not require interaction with the nucleocapsid protein in order to function during transcription. Analysis of the M2-1 protein in reducing sodium dodecyl sulfate-polyacrylamide gels revealed two major forms distinguished by their mobilities. The slower migrating form was shown to be phosphorylated, whereas the faster migrating form was not. Mutations in the Cys(3)-His(1) motif caused a change in distribution of the M2-1 protein from the slower to the faster migrating form. The data presented here show that the Cys(3)-His(1) motif of M2-1 is essential for maintaining the functional integrity of the protein.

A new approach to estimating the minimum dietary requirement of phosphorus for large rainbow trout based on nonfecal excretions of phosphorus and nitrogen

A new method was developed to estimate the minimum dietary requirement of phosphorus (P) for large fish for which conventional methods are not suitable. The method is based upon nonfecal (mainly urinary) excretion of inorganic P and total nitrogen from fish placed in a metabolic tank. In the first experiment, small and large rainbow trout (body wt 203 and 400 g, respectively) and, in the second experiment, P-sufficient, P-deficient and starved rainbow trout (different in diet history; body wt 349-390 g) were fed a constant amount (standard feeding rate) of semipurified diets with incremental P concentrations once daily at 15 degrees C. In all cases, there was no measurable excretion of P when dietary P concentration was low; however, beyond a specific dietary concentration, excretion of P increased rapidly. The point where the fish started to excrete P was assumed to be the minimum dietary requirement. By d 3 of consuming the experimental diets, the response of the fish to dietary P concentration stabilized, and excretion of P remained constant within dietary treatment groups for the subsequent sampling days (d 6, 9 and 12). The minimum dietary requirement of available P for fish having body wt of 203 and 400 g was estimated to be 6.62 and 5.54 g/kg dry diet, respectively, and that for P-sufficient, P-deficient and starved fish was estimated to be 4.06, 5.83 and 4.72 g/kg dry diet, respectively, when feed efficiency is 1.

Phosphatase activity in rat adipocytes: effects of insulin and insulin resistance

Insulin regulates the activity of both protein kinases and phosphatases. Little is known concerning the subcellular effects of insulin on phosphatase activity and how it is affected by insulin resistance. The purpose of this study was to determine insulin-stimulated subcellular changes in phosphatase activity and how they are affected by insulin resistance. We used an in vitro fatty acid (palmitate) induced insulin resistance model, differential centrifugation to fractionate rat adipocytes, and a malachite green phosphatase assay using peptide substrates to measure enzyme activity. Overall, insulin alone had no effect on adipocyte tyrosine phosphatase activity; however, subcellularly, insulin increased plasma membrane adipocyte tyrosine phosphatase activity 78 +/- 26% (n = 4, P < 0.007), and decreased high-density microsome adipocyte tyrosine phosphatase activity 42 +/- 13% (n = 4, P < 0.005). Although insulin resistance induced specific changes in basal tyrosine phosphatase activity, insulin-stimulated changes were not significantly altered by insulin resistance. Insulin-stimulated overall serine/threonine phosphatase activity by 16 +/- 5% (n = 4, P < 0.005), which was blocked in insulin resistance. Subcellularly, insulin increased plasma membrane and crude nuclear fraction serine/threonine phosphatase activities by 59 +/- 19% (n = 4, P < 0. 005) and 21 +/- 7% (n = 4, P < 0.007), respectively. This increase in plasma membrane fractions was inhibited 23 +/- 7% (n = 4, P < 0. 05) by palmitate. Furthermore, insulin increased cytosolic protein phosphatase-1 (PP-1) activity 160 +/- 50% (n = 3, P < 0.015), and palmitate did not significantly reduce this activity. However, palmitate did reduce insulin-treated low-density microsome protein phosphatase-1 activity by 28 +/- 6% (n = 3, P < 0.04). Insulin completely inhibited protein phosphatase-2A activity in the cytosol and increased crude nuclear fraction protein phosphatase-2A activity 70 +/- 29% (n = 3, P < 0.038). Thus, the major effects of insulin on phosphatase activity in adipocytes are to increase plasma membrane tyrosine and serine/threonine phosphatase, crude nuclear fraction protein phosphatase-2A, and cytosolic protein phosphatase-1 activities, while inhibiting cytosolic protein phosphatase-2A. Insulin resistance was characterized by reduced insulin-stimulated serine/threonine phosphatase activity in the plasma membrane and low-density microsomes. Specific changes in phosphatase activity may be related to the development of insulin resistance.

Evaluation of a fully automated high-performance liquid chromatography assay for hemoglobin A1c

INTRODUCTION

Measurement of hemoglobin A1c (HbA1c) is used as an objective measure of long-term blood glucose control in diabetic patients. Recent improvements in automation combined with new recommendations for precision and accuracy have caused us to reevaluate our methods for measuring HbA1c.

OBJECTIVE

We evaluated a newly automated high-performance liquid chromatography (HPLC) instrument for measurement of HbA1c (Tosoh A1c 2.2 Plus Glycohemoglobin Analyzer, Tosoh Medics, Foster City, Calif) and compared the results obtained by HPLC to those obtained with an immunoassay (Hitachi 911, Boehringer Mannheim Corporation, Indianapolis, Ind).

RESULTS

The Tosoh analyzer was found to be linear in a range of 5.3% to 17% and had a throughput of 20 samples per hour. HbA1c results for 102 patient samples by the 2 techniques showed good correlation, with a slope of 0.87 and an intercept at 1.27% +/- 0.15%. Both the total and within-run coefficients of variation were consistently lower for the HPLC method compared with the immunoassay method. The HPLC method produces a chromatogram that shows the different hemoglobin fractions, allowing identification of abnormal hemoglobin variants. In heterozygous individuals, HbA1c measurements are made with no interference from the hemoglobin variant. In the case of homozygous or doubly heterozygous hemoglobin variants, the Tosoh HPLC identifies the hemoglobin variants as such and correctly does not report a HbA1c value in the presence of a markedly decreased amount of hemoglobin A.

CONCLUSIONS

The Tosoh HPLC provides adequate throughput and improved precision, and the method is traceable to the Diabetes Control and Complications Trial.

Anterior cervical discectomy for one- and two-level cervical disc disease: the controversy surrounding the question of whether to fuse, plate, or both

Since the introduction of anterior approaches to the cervical spine for the surgical treatment of degenerative disc disease, controversies have developed regarding the necessity of fusion following anterior cervical discectomy, the use of allografts instead of autologous bone for fusion, and, recently, the employment of anterior cervical plating systems in addition to fusion for uncomplicated disc disease. We reviewed seven clinical papers dealing with these issues; these articles surveyed a total of 1153 patients. Several observations can be made from these reviews. First, there is little or no difference in clinical outcome following single-level anterior discectomy, whether a fusion is performed or not, regardless of whether the operation was for soft discs or osteophytes. Second, most patients who underwent two-level discectomies had outcomes comparable to patients who underwent surgery at one level, regardless of whether they were fused or not. Data from four prospective randomized clinical studies in addition to multiple non-randomized or retrospective studies support these conclusions. Although the incidence of complications such as persistent postoperative posterior cervical and shoulder pain and kyphotic deformities is higher in unfused patients (and is quite significant in some series), the advantages conferred by interbody fusion such as biomechanical stability, decreased incidence of kyphotic deformity, and decreased pain are offset by graft and donor-site morbidity. Specific indications for fusion include multi-level discectomies, significant straightening of the cervical spine, failed prior fusions, and trauma. It has been demonstrated that comparable fusion rates can be achieved with allografts rather than harvested autologous bone. The advantages of autografts over allografts are relatively slight in most patients who undergo anterior fusion for one- or two-level disc disease, although patients with impaired healing, significant osteopenia, or concomitant microvascular disease, such as chronic smokers, may benefit from autologous bone. The use of allografts avoids donor-site morbidity in patients without these problems. Anterior cervical plates are useful for cases of instability requiring fusion (such as trauma); these implants may decrease reoperation rates and the incidence of delayed instability in select cases. However, the cost-effectiveness of their generalized use for uncomplicated cervical disc disease has not been demonstrated. In conclusion, a general statement regarding the optimal surgical treatment for cervical disc herniations using anterior approaches is difficult to make with this limited review. Surgeons' experience and familiarity with a particular approach are probably the most important factors in ensuring successful outcomes.

Diverse gene junctions of respiratory syncytial virus modulate the efficiency of transcription termination and respond differently to M2-mediated antitermination

The ability of the diverse gene junctions of respiratory syncytial (RS) virus to signal the termination of transcription was analyzed. Nine dicistronic subgenomic replicons of RS virus were constructed; each contained one of the RS virus gene junctions in its natural upstream and downstream sequence context. The RNA synthesis activities of these subgenomic replicons were analyzed in the absence and presence of the M2 protein, which we showed previously to function as a transcription antiterminator. Our data showed that the efficiency with which the polymerase terminated transcription was affected by the gene junction that it encountered. The M2 protein significantly decreased the efficiency of the termination of transcription, resulting in increased levels of readthrough transcription at all the gene junctions. The diverse gene junctions fell into three broad groups with respect to their ability to signal transcription termination. One group of gene junctions (NS1/NS2, NS2/N, M2/L, and L/trailer) showed inefficient termination in the absence or the presence of the M2 protein. A second group of gene junctions (N/P, P/M, M/SH, SH/G, and G/F) terminated transcription efficiently. The SH/G gene junction terminated transcription with the greatest efficiency and produced low levels of readthrough transcripts in the absence or the presence of the M2 protein, correlating with the absence of SH/G polycistronic transcripts in RS virus-infected cells. The F/M2 gene junction was particularly sensitive to the M2 protein: it efficiently signaled termination in the absence of the M2 protein but produced high levels of readthrough transcripts in the presence of the M2 protein. This result suggests that the M2 protein may regulate its own production by negative feedback. The data presented here show that the different gene junctions of RS virus do modulate RS virus transcription termination. The M2 protein reduced termination at all gene junctions. The magnitude of antitermination due to the M2 protein, however, varied at the different gene junctions. The data presented here indicate that the mechanism for the regulation of RS virus gene expression is more complex than was previously appreciated.