Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells

The nucleocapsid (N) protein of several members within the order Nidovirales localizes to the nucleolus during infection and after transfection of cells with N genes. However, confocal microscopy of N protein localization in Vero cells infected with the severe acute respiratory syndrome coronavirus (SARS-CoV) or transfected with the SARS-CoV N gene failed to show the presence of N in the nucleoplasm or nucleolus. Amino acids 369 to 389, which contain putative nuclear localization signal (NLS) and nucleolar localization signal motifs, failed to restore nuclear localization to an NLS-minus mutant Rev protein. These data indicate that nuclear localization is not a conserved property among all nidoviruses.     

Viruses, masters at downsizing

Viruses are the smallest fruits on the tree of life. Dwarfed by their bacterial and cellular hosts, viruses and their close relatives have long been considered the smallest microbes. The genome of a virus may contain no more than three thousand nucleotides, compared to the three billion base pairs in human genomes. (Lest we feel superior, though, the genomes of some other organisms are much larger than our own.).     

Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses

Viruses are divided into seven classes on the basis of differing strategies for storing and replicating their genomes through RNA and/or DNA intermediates. Despite major differences among these classes, recent results reveal that the non-virion, intracellular RNA-replication complexes of some positive-strand RNA viruses share parallels with the structure, assembly and function of the replicative cores of extracellular virions of reverse-transcribing viruses and double-stranded RNA viruses. Therefore, at least four of seven principal virus classes share several underlying features in genome replication and might have emerged from common ancestors. This has implications for virus function, evolution and control.     

The role of wing length in the evolution of avian flightlessness

Flightlessness has evolved independently in at least 11 extant avian families. A number of hypotheses have been proposed to explain these transitions in individual families, including release from predation on oceanic islands, energetic costs of flight and use of forelimbs for activities other than flying. Few studies have sought to explore factors common to all families containing flightless species, which may explain the taxonomic distribution of flightlessness. In this study, we found that for all eight avian families which contain both flightless and flighted species, the flighted species have shorter wing lengths relative to body mass than their sister families. This result is not biased by taxon size. Models of avian aerodynamics predict that birds with relatively short wings pay a high energetic cost of flight. We suggest that these increased energetic costs of flying predispose these avian families to evolve flightless species. The various causes for the shortening of wings among flighted species of birds and the possibility of future transitions to flightlessness are discussed.     

Coronaviruses

Coronaviruses contain positive-stranded RNA with ca. 30 kb as a genome, which is wrapped by the envelope, and constitute Nidovirales together with Arteriviridae. The feature of viruses in Nidovirales is the unique structure of the mRNA set, called 3' co-terminal nested set. Coronaviruses have several to more than 10 different species of subgenomic mRNA and generally only the OFR located in the 5' end of each mRNA is translated. The 5' 20 kb of the coronavirus genome or mRNA-1 consists of two ORFs, 1a and 1b, between that there is a unique RNA structure called pseudoknot. From mRNA-1, 1a as well as 1a+1b are translated; the latter 1a+1b results from the translation due to ribosomal frame-shifting facilitated by the pseudoknot structure. From those two proteins, totally 16 proteins are produced as a result of auto-cleavage by the proteases included in la protein. Those proteins exhibit different functions, such as RNA-dependent RNA polymerase, helicase, proteases and proteins that regulate cellular functions, mRNAs smaller than mRNA-2 translate in general the structural proteins, nucleocapsid (N) protein, spike (S) protein, integrated membrane (M) protein and envelope (E) proteins. Those proteins assemble to the vesicles located from ER to Golgi (ER Golgi intermediate compartment) and virions bud into the vesicles. Those virions are released from infected cells via exocytosis.     

Viruses and the nucleolus: The fatal attraction

Viruses are small obligatory parasites and as a consequence, they have developed sophisticated strategies to exploit the host cell's functions to create an environment that favors their own replication. A common feature of most – if not all – families of human and non-human viruses concerns their interaction with the nucleolus. The nucleolus is a multifunctional nuclear domain, which, in addition to its well-known role in ribosome biogenesis, plays several crucial other functions. Viral infection induces important nucleolar alterations. Indeed, during viral infection numerous viral components localize in nucleoli, while various host nucleolar proteins are redistributed in other cell compartments or are modified, and non-nucleolar cellular proteins reach the nucleolus. This review highlights the interactions reported between the nucleolus and some human or animal viral families able to establish a latent or productive infection, selected on the basis of their known interactions with the nucleolus and the nucleolar activities, and their links with virus replication and/or pathogenesis. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.     

Viruses and the Advantage of Sex in Anthoxanthum odoratum: A Review

Abstract The nature of the selective forces responsible for the maintenance of sexual reproduction in populations remains controversial. Theoreticians have proposed a variety of mechanisms to explain how sex is adaptive, including varying environments, sib competition, mutational damage, and pathogens. In a well-studied population of the short-lived, perennial grass Anthoxanthum odoratum in a mown North Carolina field, significant fitness advantages for sexual vs. asexual offspring have been shown. Evidence from two recent experiments implicates barley yellow dwarf luteovirus (BYDV), a single-stranded RNA virus, as a cause of the short-term advantage for sex in this population. When planted in sites close to parents, asexual offspring were twice as frequently infected as sexual offspring. In other sites, infection was more frequent among common than rare genotypes. Viruses possess a unique combination of features which make them plausible candidates to favor sexual reproduction in plants. Viruses are pervasive, have subtle but significant fitness effects, have the potential for rapid mutation and evolution, and are spread by vectors whose behaviors are host frequency dependent. The ecological and evolutionary consequences of viruses in plant populations deserve further study.     

Cytokine receptors and signal transduction.

Most of the recently cloned cytokine receptors that operate in the immune and hematopoietic systems contain no tyrosine kinase domains in their cytoplasmic regions, unlike the family of growth factor receptors defined earlier. However, they can be assigned to several new types of receptor families based on structural similarities among them. It is characteristic of these receptors that many of them require a receptor-associated molecule in order to achieve high-affinity ligand binding and/or transmission of cytoplasmic signals. Receptor-associated molecules have been found that transduce cytoplasmic signals and are shared by different cytokine receptors. Phosphorylation of the receptors and of various cytoplasmic proteins after ligand stimulation seems to be a common event in cytokine systems. Insight into the pleiotropic and redundant nature of cytokine action is provided by the discovery of several new cytokine receptor families and of shared signal transduction molecules and by the idea that several cytoplasmic kinases may be able to functionally substitute for one another in transmitting cytokine signals.     

Correlations between flavonoid chemistry,anatomy and geography in the restionaceae

Comparisons of the flavonoid patterns in stems and inflorescences between Australasian and South African members of the Restionaceae indicate significant differences with geography. Nine of 14 Australasian species contain gossypetin or a related 8-hydroxyflavonoid and proanthocyanidins are uncommon. By contrast, the 33 South African taxa studied contain common flavonols, flavones and glycoflavones, while proanthocyanidins are present in 29. Two anatomically related South African genera, Chondropetalum and Elegia, contain, in addition, myricetin 3-galactoside, together with the 3-galactosides of the myricetin methyl ethers, larycitrin and syringetin. These results confirm the conclusions derived from anatomy that members of Hypolaena, Leptocarpus and Restio, genera represented in both Australia and South Africa, have the distinctive flavonoids characteristic of their geographic origin rather than of their systematic position. The family as a whole is different in flavonoid pattern from other monocotyledonous families with which it is sometimes associated.     

beta-fructosidase superfamily: homology with some alpha-L-arabinases and beta-D-xylosidases

Comparison of the amino acid sequences of four families of glycosyl hydrolases reveals that they are homologous and have several common conserved regions. Two of these families contain beta-fructosidases (glycosyl hydrolase families GH32 and GH68) and the other two include alpha-L-arabinases and beta-xylosidases (families GH43 and GH62). The latter two families are proposed to be grouped together with the former two into the beta-fructosidase (furanosidase) superfamily. Several ORFs can be considered as a fifth family of the superfamily on the basis of sequence similarity. It is shown for the first time that a glycosyl hydrolase superfamily can include enzymes with both inversion and retention mechanism of action. Composition of the active center for enzymes of the superfamily is discussed.     

Viral Detection: Past,Present, and Future

Viruses are essentially composed of a nucleic acid (segmented or not, DNA, or RNA) and a protein coat. Despite their simplicity, these small pathogens are responsible for significant economic and humanitarian losses that have had dramatic consequences in the course of human history. Since their discovery, scientists have developed different strategies to efficiently detect viruses, using all possible viral features. Viruses shape, proteins, and nucleic acid are used in viral detection. In this review, the development of these techniques, especially for plant and mammalian viruses, their strengths and weaknesses as well as the latest cutting‐edge technologies that may be playing important roles in the years to come are described.     

Viruses of the extremely thermophilic archaeon Sulfolobus

Viruses of Sulfolobus are highly unusual in their morphology, and genome structure and sequence. Certain characteristics of the replication strategies of these viruses and the virus-host interactions suggest relationships with eukaryal and bacterial viruses, and the primeval existence of common ancestors. Moreover, studying these viruses led to the discovery of archaeal promoters and has provided tools for the development of the molecular genetics of these organisms. The Sulfolobus viruses contain unique regulatory features and structures that undoubtedly hold surprises for researchers in the future.     

新疆蝗总科区系研究

新疆现有蝗虫１５７种,它们分别隶属于８科６２属。在１５７种蝗虫中,古北种占绝对优势,有１２０种,其次为特有种,有３５种,广布种甚少,仅２种。在古北种中,中亚种最多,其次为泛古北种,而欧洲西伯利亚种、地中海种和东北种均很少。在８个科中,泛古北种在网翅蝗科中占优势,中亚种在班翅蝗科中占优势,斑腿蝗科在蝗总科中是相当大的一个科,在我国也占有很大优势,但在新疆其属种数量却很少。     

Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater

Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.     

The role of electron microscopy in the rapid diagnosis of viral infections — <Emphasis Type="Italic">review</Emphasis>

Electron microscopy (EM) allows fast visualization of viruses in a wide range of clinical specimens. Viruses are grouped into families based on their morphology. Viruses from various families look distinctly and these morphological variances are the basis for identification of viruses by EM. The identification to the family level is often sufficient for the clinician or recognition of an unknown infectious agent. Diagnostic EM has two advantages over enzyme-linked immunosorbent assay and nucleic acid amplification tests. After a simple and fast negative staining, EM allows fast morphological identification and differential diagnosis of infectious agents contained in the specimen without the need for special considerations and/or reagents. Nevertheless, EM has the disadvantage of being unsuitable as a screening method.     

Sesqui-, di-, and triterpenoids as chemosystematic markers in extant conifers—A review

Chemosystematics is a common tool in systematics and taxonomy of extant plants. Terpenoids have been found to be especially valuable for chemosystematic investigations of conifers. A review of data in the extensive literature revealed some characteristic distribution patterns of sesqui-, di-, and triterpenoids in extant conifer families. The numerous terpenoids can be assigned to approximately 40 sesquiterpenoid, 17 diterpenoid, and only a few triterpenoid structural classes. Some of these terpenoid classes (e.g., cadinanes, humulanes, labdanes, pimaranes) are unspecific and distributed among all conifers. Other structural classes occur in certain clusters of families (e.g., totaranes in Podocarpaceae, Taxodiaceae, and Cupressaceae s.str.) or were restricted to species of only one conifer family (e.g., cuparanes in Cupressaceae s.str.). Cupressaceae s.str. and Taxodiaceae show great similarities in their terpenoid composition (cedranes, thujopsanes) but can be separated by the occurrence of some sesquiterpenoids (cuparanes, widdranes), which were hitherto known only in Cupressaceae s.str. This supports a monophyletic clade of Cupressaceae s.str. within the major Taxodiaceae/Cupressaceae lineage (= Cupressaceae s.l.). Pinaceae differ from the other conifer families because they commonly lack several diterpenoid classes (phenolic abietanes, tetracyclic diterpenoids) and because they contain some distinct sesquiterpenoids (longicyclanes, sativanes), diterpenoids (cembranes), and triterpenoids (serratanes, lanostanes). With the exception of diterpenoid alkaloids (taxanes), Taxaceae contain terpenoids common in the other conifer families. This supports their inclusion as a separate family in the major conifer clade.     

B chromosomes: an update about their occurrence in freshwater Neotropical fishes (Teleostei)

In freshwater Neotropical fishes, supernumerary chromosomes or B chromosomes have been found in 61 species so far, distributed in 16 families of seven different orders and in distinct hydrographic basins. The order Characiformes is the one that possesses the most species with these chromosomes, including 31 species from six different families. The order Siluriformes has 21 species from five families, with Rhamdia , of the family Heptapteridae, being the most common genus where these chromosomes are found. The order Perciformes has five species with B chromosomes in only one family, Cichlidae, and the orders Beloniformes, Cyprinodontiformes, Gymnotiformes and Synbranchiformes contain only one species each with extra chromosomes. They are found as microchromosomes in Schizodon , Astyanax , Moenkhausia , Cyphocharax , Steindachnerina , Prochilodus , Rhamdia , Iheringichthys and Loricaria , among others, up to supernumerary macrochromosomes as in Astyanax , varying in morphology as well as number, showing evidence of the wide diversity of B chromosomes in Neotropical fishes.     

CD spectra show the relational style between Zic-, Gli-, Glis-zinc finger protein and DNA

Zic family proteins have five C2H2-type zinc finger motifs. The Zic-zinc finger domains show high homology to the corresponding domains of the Gli and Glis families, which also contain five C2H2-type zinc finger motifs. The zinc finger motifs of the proteins of these three protein families form an alpha-helix conformation in solution. The addition of oligo DNA that included a Gli-binding sequence increased the alpha-helix content estimated by using circular dichroism spectroscopy. Comparison of the Zic-, Gli-, and Glis-zinc fingers indicated that the alpha-helix content after the addition of oligo DNA correlated well with the affinity of each zinc finger for the oligo DNA (correlation coefficient, 0.85). The importance of the zinc ion for protein folding was reflected in a reduction in the alpha-helix content upon removal of the zinc ion. Owing to the compact globular structure, the alpha-helix structure of the proteins of these three protein families is extremely thermally stable. These results suggest that the alpha-helix structure is important for DNA binding and profoundly related to functional and structural diversity among the three families.