Fowlpox Virus Encodes Nonessential Homologs of Cellular Alpha-SNAP, PC-1, and an Orphan Human Homolog of a Secreted Nematode Protein

The genome of fowlpox virus (FWPV), type species of the Avipoxviridae, is considerably rearranged compared with that of vaccinia virus (the prototypic poxvirus and type species of the Orthopoxviridae) and is 30% larger. It is likely that the genome of FWPV contains genes in addition to those found in vaccinia virus, probably involved with its replication and survival in the chicken. A 7,470-bp segment of the FWPV genome has five open reading frames (ORFs), two of which encode ankyrin repeat proteins, many examples of which have been found in poxviruses. The remaining ORFs encode homologs of cellular genes not reported in any other virus. ORF-2 encodes a homolog of the yeast Sec17p and mammalian SNAP proteins, crucial to vesicular transport in the exocytic pathway. ORF-3 encodes a homolog of an orphan human protein, R31240_2, encoded on 19p13.2. ORF-3 is also homologous to three proteins (YLS2, YMV6, and C07B5.5) from the free-living nematode Caenorhabditis elegans and to a 43-kDa antigen from the parasitic nematode Trichinella spiralis. ORF-5 encodes a homolog of the mammalian plasma cell antigen PC-1, a type II glycoprotein with exophosphodiesterase activity. The ORFs are present in the virulent precursor, HP1, of the sequenced attenuated virus (FP9) and are conserved in other strains of FWPV. They were shown, by deletion mutagenesis, to be nonessential to virus replication in tissue culture. RNA encoding the viral homolog of PC-1 is expressed strongly early and late in infection, but RNAs encoding the homologs of SNAP and R31240_2 are expressed weakly and late.     

Complete Genomic Sequence of Bacteriophage φEcoM-GJ1, a Novel Phage That Has Myovirus Morphology and a Podovirus-Like RNA Polymerase

The complete genome of EcoM-GJ1, a lytic phage that attacks porcine enterotoxigenic Escherichia coli of serotype O149:H10:F4, was sequenced and analyzed. The morphology of the phage and the identity of the structural proteins were also determined. The genome consisted of 52,975 bp with a G+C content of 44% and was terminally redundant and circularly permuted. Seventy-five potential open reading frames (ORFs) were identified and annotated, but only 29 possessed homologs. The proteins of five ORFs showed homology with proteins of phages of the family Myoviridae, nine with proteins of phages of the family Podoviridae, and six with proteins of phages of the family Siphoviridae. ORF 1 encoded a T7-like single-subunit RNA polymerase and was preceded by a putative E. coli σ⁷⁰-like promoter. Nine putative phage promoters were detected throughout the genome. The genome included a tRNA gene of 95 bp that had a putative 18-bp intron. The phage morphology was typical of phages of the family Myoviridae, with an icosahedral head, a neck, and a long contractile tail with tail fibers. The analysis shows that EcoM-GJ1 is unique, having the morphology of the Myoviridae, a gene for RNA polymerase, which is characteristic of phages of the T7 group of the Podoviridae, and several genes that encode proteins with homology to proteins of phages of the family Siphoviridae.     

Neonicotinoid-Coated Zea mays Seeds Indirectly Affect Honeybee Performance and Pathogen Susceptibility in Field Trials

Thirty-two honeybee (Apis mellifera) colonies were studied in order to detect and measure potential in vivo effects of neonicotinoid pesticides used in cornfields (Zea mays spp) on honeybee health. Honeybee colonies were randomly split on four different agricultural cornfield areas located near Quebec City, Canada. Two locations contained cornfields treated with a seed-coated systemic neonicotinoid insecticide while the two others were organic cornfields used as control treatments. Hives were extensively monitored for their performance and health traits over a period of two years. Honeybee viruses (brood queen cell virus BQCV, deformed wing virus DWV, and Israeli acute paralysis virus IAPV) and the brain specific expression of a biomarker of host physiological stress, the Acetylcholinesterase gene AChE, were investigated using RT-qPCR. Liquid chromatography-mass spectrometry (LC-MS) was performed to detect pesticide residues in adult bees, honey, pollen, and corn flowers collected from the studied hives in each location. In addition, general hive conditions were assessed by monitoring colony weight and brood development. Neonicotinoids were only identified in corn flowers at low concentrations. However, honeybee colonies located in neonicotinoid treated cornfields expressed significantly higher pathogen infection than those located in untreated cornfields. AChE levels showed elevated levels among honeybees that collected corn pollen from treated fields. Positive correlations were recorded between pathogens and the treated locations. Our data suggests that neonicotinoids indirectly weaken honeybee health by inducing physiological stress and increasing pathogen loads.     

Infections of Nosema ceranae in four different honeybee species

The microsporidium Nosema ceranae is detected in honeybees in Thailand for the first time. This endoparasite has recently been reported to infect most Apis mellifera honeybee colonies in Europe, the US, and parts of Asia, and is suspected to have displaced the endemic endoparasite species, Nosema apis, from the western A. mellifera. We collected and identified species of microsporidia from the European honeybee (A. mellifera), the cavity nesting Asian honeybee (Apis cerana), the dwarf Asian honeybee (Apis florea) and the giant Asian honeybee (Apis dorsata) from colonies in Northern Thailand. We used multiplex PCR technique with two pairs of primers to differentiate N. ceranae from N. apis. From 80 A. mellifera samples, 62 (77.5%) were positively identified for the presence of the N. ceranae. Amongst 46 feral colonies of Asian honeybees (A. cerana, A. florea and A. dorsata) examined for Nosema infections, only N. ceranae could be detected. No N. apis was found in our samples. N. ceranae is found to be the only microsporidium infesting honeybees in Thailand. Moreover, we found the frequencies of N. ceranae infection in native bees to be less than that of A. mellifera.     

Fertility and reproductive rate of Varroa mite,Varroa destructor,in native and exotic honeybee,Apis mellifera L., colonies under Saudi Arabia conditions

Varroa mite is the most destructive pest to bee colonies worldwide. In Saudi Arabia, preliminary data indicated high infestation levels in the exotic honeybee colonies; such as Apis mellifera carnica and Apis mellifera ligustica, compared to native honeybee subspecies Apis mellifera jemenitica, which may imply higher tolerance to Varroasis. In this study, fertility and reproductive rate of Varroa mite, Varroa destructor, in capped brood cells of the native honeybee subspecies were investigated and compared with an exotic honeybee subspecies, A. m. carnica. Mite fertility was almost alike (87.5% and 89.4%) in the native and craniolan colonies respectively. Similarly, results did not show significant differences in reproduction rate between both subspecies (F = 0.66, Pr > F = 0.42). Number of adult Varroa daughters per fertile mother mite was 2.0 and 2.1 for native and craniolan honeybee subspecies respectively. This may indicate that mechanisms of keeping low infestation rates in the native honeybee colonies are not associated with Varroa reproduction. Therefore, potential factors of keeping lower Varroa infestation rates in native honey bee subspecies should be further investigated.     

Response of foster Asian honeybee (Apis cerana Fabr.) colonies to the brood of European honeybee (Apis mellifera L.) infested with parasitic mite,Varroa jacobsoni oudemans

The response of Asian honeybee (Apis cerana Fabr.) colonies toward the introduced worker brood of the European honeybee (Apis mellifera L.) infested with the parasitic mite Varroa jacobsoni Oudemans was investigated. When no mites were present, 40% of the healthy open brood and 3% of the healthy capped brood of the European honeybees were rejected by the Asian honeybee colonies. When the brood was infested, brood rejection was significantly higher for open (P < 0.05) and capped broods (P < 0.01). The brood removal activity decreased with time. The quantity of brood removed was also correlated with mite infestation level for open (r² = 0.933) and sealed broods (r² = 0.918). The feasibility of using heterospecific colonies to control Varroa mite is unclear and is discussed from behavioral and ecological points of view.     

High Concentrations of the Alarm Pheromone Component,Isopentyl Acetate,Reduces Foraging and Dancing in <Emphasis Type="Italic">Apis mellifera</Emphasis> Ligustica and <Emphasis Type="Italic">Apis cerana</Emphasis> Cerana

A honeybee colony is a superorganism that has evolved precise communication systems, which allow the colony to gather information from numerous individuals and coordinate its behavior. Alarm pheromones, such as isopentyl acetate (IPA), the main component of sting alarm pheromone, play a critical role in the coordination of individual behaviors as well as colony communication in honeybee colonies. In this study, honeybees (Apis mellifera ligustica and Apis cerana cerana) were exposed to relatively high levels of IPA at a foraging site (6–8 bee equivalents) and inside their colony (28–58 bee equivalents) to investigate the influence of alarm pheromones on foraging activity and hive flight activity. IPA reduced the number of bees that flew out the hive, foraged, and waggle danced. Under both contexts in the hive and at the food source, IPA can therefore inhibit honey bee foraging and foraging communication.     

Complete genomic sequence of bacteriophage phiEcoM-GJ1, a novel phage that has myovirus morphology and a podovirus-like RNA polymerase

The complete genome of phiEcoM-GJ1, a lytic phage that attacks porcine enterotoxigenic Escherichia coli of serotype O149:H10:F4, was sequenced and analyzed. The morphology of the phage and the identity of the structural proteins were also determined. The genome consisted of 52,975 bp with a G+C content of 44% and was terminally redundant and circularly permuted. Seventy-five potential open reading frames (ORFs) were identified and annotated, but only 29 possessed homologs. The proteins of five ORFs showed homology with proteins of phages of the family Myoviridae, nine with proteins of phages of the family Podoviridae, and six with proteins of phages of the family Siphoviridae. ORF 1 encoded a T7-like single-subunit RNA polymerase and was preceded by a putative E. coli sigma(70)-like promoter. Nine putative phage promoters were detected throughout the genome. The genome included a tRNA gene of 95 bp that had a putative 18-bp intron. The phage morphology was typical of phages of the family Myoviridae, with an icosahedral head, a neck, and a long contractile tail with tail fibers. The analysis shows that phiEcoM-GJ1 is unique, having the morphology of the Myoviridae, a gene for RNA polymerase, which is characteristic of phages of the T7 group of the Podoviridae, and several genes that encode proteins with homology to proteins of phages of the family Siphoviridae.     

Cotesia plutellae Bracovirus Genome and Its Function in Altering Insect Physiology

Polydnavirus is a group of animal DNA virus mutually associated with some ichneumonoid wasp. Its relatively large size of genome has been considered as a major source of the parasitoid function to manipulate developmental and immunological processes of target parasitized insects. Cotesia plutellae bracovirus (CpBV) is a polydnavirus derived from C. plutellae, which parasitizes the diamondback moth, Plutella xylostella. Parasitized P. xylostella exhibits altered physiological symptoms in development and immune reactions. Though several other parasitic factors such as ovarian proteins, venom, and teratocytes are identified, CpBV has been more focused on elucidating various host physiological alterations occurring due to the parasitism, which has driven the CpBV genome project. CpBV attains a typical bracovirus structure by its single unit membrane envelope, in which multiple nucleocapsids are enclosed. Its genome DNAs are segmented and located on the genome of C. plutellae. Its replication begins at adult tissue development during pupal stage. An apparent genome size is 471 kb estimated from 27 segments separated on 5% agarose gel. A current work on the genome has been completely sequenced 24 genomic segments and analyzed their genomic structure. The aggregated genome size is 351, 299 bp long and exhibits an average GC content of approximately 34.6%. Average coding density is about 32.3% and 125 putative open reading frames are predicted. Though more than half (52.5%) of predicted genes are annotated as hypothetical, the annotated CpBV genes share amino acid sequence homologies with those of other bracoviral genomes. The annotated genes are classified into the known bracoviral families, in which a family of protein tyrosine phosphatase is the largest including 36 ORFs, suggesting a significant role during parasitization. In addition, 8 and 7 ORFs encode Iκβ-like and EP1-like, respectively. Some predicted genes are known only in Cotesia-associated bracoviral genomes. Finally, two homologous genes, CpBV15α/β, are unique in CpBV genome, which are not matched to any other known polydnaviral genes. Their homology with malarian circumsporozoite toxin and eukaryotic translation inhibition factors suggests their function in host translation inhibitory factor. This review discusses CpBV genes on their putative physiological functions based on the molecular interactions between the host-parasite.     

On the Front Line: Quantitative Virus Dynamics in Honeybee (Apis mellifera L.) Colonies along a New Expansion Front of the Parasite Varroa destructor

Over the past fifty years, annual honeybee (Apis mellifera) colony losses have been steadily increasing worldwide. These losses have occurred in parallel with the global spread of the honeybee parasite Varroa destructor. Indeed, Varroa mite infestations are considered to be a key explanatory factor for the widespread increase in annual honeybee colony mortality. The host-parasite relationship between honeybees and Varroa is complicated by the mite''s close association with a range of honeybee viral pathogens. The 10-year history of the expanding front of Varroa infestation in New Zealand offered a rare opportunity to assess the dynamic quantitative and qualitative changes in honeybee viral landscapes in response to the arrival, spread and level of Varroa infestation. We studied the impact of de novo infestation of bee colonies by Varroa on the prevalence and titres of seven well-characterised honeybee viruses in both bees and mites, using a large-scale molecular ecology approach. We also examined the effect of the number of years since Varroa arrival on honeybee and mite viral titres. The dynamic shifts in the viral titres of black queen cell virus and Kashmir bee virus mirrored the patterns of change in Varroa infestation rates along the Varroa expansion front. The deformed wing virus (DWV) titres in bees continued to increase with Varroa infestation history, despite dropping infestation rates, which could be linked to increasing DWV titres in the mites. This suggests that the DWV titres in mites, perhaps boosted by virus replication, may be a major factor in maintaining the DWV epidemic after initial establishment. Both positive and negative associations were identified for several pairs of viruses, in response to the arrival of Varroa. These findings provide important new insights into the role of the parasitic mite Varroa destructor in influencing the viral landscape that affects honeybee colonies.     

Comparison of the activity and productivity of Carniolan (Apis mellifera carnica Pollmann) and Yemeni (Apis mellifera jemenitica Ruttner) subspecies under environmental conditions of the Al-Ahsa oasis of eastern Saudi Arabia

This study was conducted at the apiary of the Agricultural and Veterinary Training and Research Station of King Faisal University in the Al-Ahsa oasis of eastern Saudi Arabia. We performed a comparison between Carniolan (Apis mellifera carnica Pollmann) and Yemeni (Apis mellifera jemenitica Ruttner) honeybee races to determine the monthly fluctuations in foraging activity, pollen collection, colony growth and honey yield production under the environmental conditions of the Al-Ahsa oasis of eastern Saudi Arabia. We found three peaks in the flight activity of the two races, and the largest peaks occurred during September and October. Compared to Carniolan bee colonies, the performance of Yemeni bee colonies was superior in terms of stored pollen, worker and drone brood rearing, and the adult population size. The Carniolan bee colonies produced 27.77% and 27.50% more honey than the Yemeni bee colonies during the flow seasons of alfalfa and sidir, respectively, with an average increase of 27.64%. It could be concluded that the race of bees is an important factor affecting the activity and productivity of honeybee colonies. The Yemeni bee race produced more pollen, a larger brood and more bees, which exhibited a longer survival. The imported Carniolan bees can be reared in eastern Saudi Arabia, but the Yemeni bee race is still better.     

Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.

The 2694 ORFs originally annotated as potential genes in the genome of Aeropyrum pernix can be categorized into three clusters (A, B, C), according to their nucleotide composition at three codon positions. Coding potential was found to be responsible for the phenomenon of three clusters in a 9-dimensional space derived from the nucleotide composition of ORFs: ORFs assigned to cluster A are coding ones, while those assigned to clusters B and C are non-coding ORFs. A "codingness" index called the AZ score is defined based on a clustering method used to recognize protein-coding genes in the A. pernix genome. The criterion for a coding or non-coding ORF is based on the AZ score. ORFs with AZ > 0 or AZ < 0 are coding or non-coding, respectively. Consequently, 620 out of 632 ORFs with putative functions based on the original annotation are contained in cluster A, which have positive AZ scores. In addition, all 29 ORFs encoding putative or conserved proteins newly added in RefSeq annotation also have positive AZ scores. Accordingly, the number of re-recognized protein-coding genes in the A. pernix genome is 1610, which is significantly less than 2694 in the original annotation and also much less than 1841 in the RefSeq annotation curated by NCBI staff. Annotation information of re-recognized genes and their AZ scores are available at: http://tubic.tju.edu.cn/Aper/.     

Genomic organization and molecular characterization of Clostridium difficile bacteriophage PhiCD119

In this study, we have isolated a temperate phage (PhiCD119) from a pathogenic Clostridium difficile strain and sequenced and annotated its genome. This virus has an icosahedral capsid and a contractile tail covered by a sheath and contains a double-stranded DNA genome. It belongs to the Myoviridae family of the tailed phages and the order Caudovirales. The genome was circularly permuted, with no physical ends detected by sequencing or restriction enzyme digestion analysis, and lacked a cos site. The DNA sequence of this phage consists of 53,325 bp, which carries 79 putative open reading frames (ORFs). A function could be assigned to 23 putative gene products, based upon bioinformatic analyses. The PhiCD119 genome is organized in a modular format, which includes modules for lysogeny, DNA replication, DNA packaging, structural proteins, and host cell lysis. The PhiCD119 attachment site attP lies in a noncoding region close to the putative integrase (int) gene. We have identified the phage integration site on the C. difficile chromosome (attB) located in a noncoding region just upstream of gene gltP, which encodes a carrier protein for glutamate and aspartate. This genetic analysis represents the first complete DNA sequence and annotation of a C. difficile phage.     

Genome of Cnaphalocrocis medinalis Granulovirus,the First Crambidae-Infecting Betabaculovirus Isolated from Rice Leaffolder to Sequenced

Cnaphalocrocis medinalis is a major pest of rice in South and South-East Asia. Insecticides are the major means farmers use for management. A naturally occurring baculovirus, C. medinalis granulovirus (CnmeGV), has been isolated from the larvae and this has the potential for use as microbial agent. Here, we described the complete genome sequence of CnmeGV and compared it to other baculovirus genomes. The genome of CnmeGV is 112,060 base pairs in length, has a G+C content of 35.2%. It contains 133 putative open reading frames (ORFs) of at least 150 nucleotides. A hundred and one (101) of these ORFs are homologous to other baculovirus genes including 37 baculovirus core genes. Thirty-two (32) ORFs are unique to CnmeGV with no homologues detected in the GeneBank and 53 tandem repeats (TRs) with sequence length from 25 to 551 nt intersperse throughout the genome of CnmeGV. Six (6) homologous regions (hrs) were identified interspersed throughout the genome. Hr2 contains 11 imperfect palindromes and a high content of AT sequence (about 73%). The unique ORF28 contains a coiled-coil region and a zinc finger-like domain of 4–50 residues specialized by two C2C2 zinc finger motifs that putatively bound two atoms of zinc. ORF21 encoding a chit-1 protein suggesting a horizontal gene transfer from alphabaculovirus. The putative protein presents two carbohydrate-binding module family 14 (CBM_14) domains rather than other homologues detected from betabaculovirus that only contains one chit-binding region. Gene synteny maps showed the colinearity of sequenced betabaculovirus. Phylogenetic analysis indicated that CnmeGV grouped in the betabaculovirus, with a close relation to AdorGV. The cladogram obtained in this work grouped the 17 complete GV genomes in one monophyletic clade. CnmeGV represents a new crambidae host-isolated virus species from the genus Betabaculovirus and is most closely relative of AdorGV. The analyses and information derived from this study will provide a better understanding of the pathological symptoms caused by this virus and its potential use as a microbial pesticide.