Genetic Diversity in RNA Virus Quasispecies Is Controlled by Host-Virus Interactions

Many RNA viruses have genetically diverse populations known as quasispecies. Important biological characteristics may be related to the levels of diversity in the quasispecies (quasispecies cloud size), including adaptability and host range. Previous work using Tobacco mosaic virus and Cucumber mosaic virus indicated that evolutionarily related viruses have very different levels of diversity in a common host. The quasispecies cloud size for these viruses remained constant throughout serial passages. Inoculation of these viruses on a number of hosts demonstrated that quasispecies cloud size is not constant for these viruses but appears to be dependent on the host. The quasispecies cloud size remained constant as long as the viruses were maintained on a given host. Shifting the virus between hosts resulted in a change in cloud size to levels associated with the new host. Quasispecies cloud size for these viruses is related to host-virus interactions, and understanding these interactions may facilitate the prediction and prevention of emerging viral diseases.     

烟草microRNA171c的功能分析

MicroRNA是一类长度为20~24碱基的非编码小RNA,调控植物多种生理代谢途径。MicroRNA171(miR171)在拟南芥、大麦和水稻中通过负调控SCL靶基因使植物表现出分枝结构变化和其他一些发育表型,还可调控拟南芥叶绿素的合成代谢。但其他植物miR171的功能仍然未知。为了探明烟草miR171c的功能,本研究根据烟草miR171c序列设计了靶基因模拟物STTM171,通过病毒表达载体在烟草中进行表达,抑制miR171c的活性后观察植物表型变化。结果表明在病毒表达STTM171烟草中,植株出现顶端优势丧失、茎干增多等表型。荧光定量PCR检测到STTM171过表达植株miR171c表达量下降,两个推测的SCL靶基因TC134811和TC127385表达量上升,表明miR171c可能在烟草和拟南芥等植物中的功能比较保守,可以通过调控可能的靶基因SCL来调节植物的生长发育。     

Determinants of Functional MicroRNA Targeting

MicroRNAs (miRNAs) play cardinal roles in regulating biological pathways and processes, resulting in significant physiological effects. To understand the complex regulatory network of miRNAs, previous studies have utilized massive-scale datasets of miRNA targeting and attempted to computationally predict the functional targets of miRNAs. Many miRNA target prediction tools have been developed and are widely used by scientists from various fields of biology and medicine. Most of these tools consider seed pairing between miRNAs and their mRNA targets and additionally consider other determinants to improve prediction accuracy. However, these tools exhibit limited prediction accuracy and high false positive rates. The utilization of additional determinants, such as RNA modifications and RNA-binding protein binding sites, may further improve miRNA target prediction. In this review, we discuss the determinants of functional miRNA targeting that are currently used in miRNA target prediction and the potentially predictive but unappreciated determinants that may improve prediction accuracy.     

Physiology of Rice Tungro Virus Disease: Involvement of Abscisic Acid-Like Substance in Susceptible Host-Virus Interactions

Stunting was severe in susceptible rice (Oryza saliva L.) cultivar ‘Taichung Native 1’ infected with tungro virus (RTV) compared to less-susceptible cultivar ‘IR 20’. The senescence of detached leaves of RTV-infected susceptible cultivar incubated in water in dark was accelerated compared to the healthy leaves as measured by the loss of total chlorophyll content. The transpiration rate of RTV-infected leaves of the susceptible cultivar was much lower than the healthy and RTV-infected leaves of the less-susceptible cultivar. Partially purified extracts obtained from RTV-infected leaves effectively inhibited GA-induced α-amylase synthesis in barley endosperms, and rice seedling growth, and they accelerated senescence of detached rice leaves. In all the three bibassays the ABA-like activity was significantly greater in the extracts from the RTV-infected susceptible cultivar than in extracts from the less-susceptible cultivar.     

Computerized Analysis of Crustacean Relationships

The strengths and weaknesses of phylogenetic analysis using computers are reviewed from the viewpoint of understanding crustacean evolution. Computerized methods require the explicit presentation of characters and character state homologies. New techniques allow investigators to design evolutionary models into a character data matrix, or to use evolutionary models that make minimal a priori assumptions. The computer analysis relieves the investigator from the highly repetitious testing of trees, allows the concentration on the character state data, and provides objective methods for comparing trees, primarily their length. These are regarded as the strengths of computerized methods. The weaknesses of these methods include the relatively inscrutable nature of the character data matrix compared with the overall ‘gestalt’ of resulting trees, the difficulties of defining discrete homologies within the Crustacea, especially for counts of segmentation, the lack of clear intermediate character states in some multistate segmental characters, and the inability to define evolutionary polarity. These difficulties may be overcome by analysing the data using the minimal assumption models of character evolution, and by a recognition that the trees are a result of the input data, and therefore the data should be criticized, rather than the trees themselves. A ‘consensus’ character data set, including most extant major groups of the Crustacea as well as several key fossils, was assembled and revised by the participants in the workshop. An artificial taxon, ‘ur-crustacean characters’, was introduced to root the tree. Three observations may be made from parsimony analyses using several weighting and tree rooting methods. (1) The currently accepted large scale phylogeny and classification of the Crustacea is not corroborated. (2) The number of supposed plesiomorphic traits possessed by a taxon is not a good index for early derivation in crustacean evolution. (3) The taxon Maxillopoda is not supported by the arrangement of any of the trees.     

Functional and Structural Parallels in Crustacean and Drosophila Neuromuscular Systems

Comparison of morphological and physiological phenotypes ofrepresentative crustacean motor neurons, and selected motorneurons of Drosophila larval abdominal muscles, shows severalfeatures in common. Crustacean motor nerve terminals, and thoseof Drosophila, possess numerous small synapses with well-definedactive zones. In crustaceans, neurons that are more tonicallyactive have markedly varicose terminals; synapses and mitochondriaare selectively localized in the varicosities. Phasic motoraxons have filiform terminals, sometimes with small varicosities;mitochondrial content is less than for tonic axons, and synapsesare distributed along the terminals. Tonic axons generate smallexcitatory potentials which facilitate strongly at higher frequencies,and which are resistant to depression. Thephasic neurons generatelarge excitatory potentials which exhibit relatively littlefrequency facilitation, and depress rapidly. In Drosophila,counterparts of crustacean phasic and tonic motor neurons havebeen found, but the differentiation is less pronounced. It isinferredthat cellular factors regulating the number of participatingsynapses and the probability of quantal release are similarin crustaceans and Drosophila, and that advantage can be takenof this in future to develop experiments addressing the regulationof synaptic plasticity.     

Host-Virus Interactions in Escherichia coli: Effect of Stationary Phase on Viral Release from MS2-Infected Bacteria

Infection of stationary-phase Escherichia coli with MS2 bacteriophage results in the production, but not the release, of progeny virus by the host. Substantial protein synthesis in stationary-phase cells indicates that general protein synthesis is not sufficient to assure cell lysis or viral release.     

Rapid Functional Analysis in Xenopus Oocytes of Po Protein Adhesive Interactions

We have developed a coupled Xenopus oocyte expression system for evaluating the functional effects of mutations in known or suspected adhesion molecules, which allows for a very rapid assessment of intercellular adhesion. As a model protein, we first used Protein zero (Po), an adhesion molecule that mediates self-adhesion of the Schwann cell plasma membrane to form compact myelin in the mammalian PNS. A wide variety of mutations in Po cause certain human peripheral neuropathies, such as the Charcot-Marie-Tooth disease (CMT) type 1B and Dejerine-Sottas syndrome (DSS). After wild-type Po mRNA is injected, the protein is synthesized and correctly targeted to the oocyte cell surface. When two oocytes are paired, wild-type Po redistributes and concentrates at the cell-cell apposition region, and by electron microscopy, the oocyte pairs show close cell-cell appositions and are devoid of the microvilli that are observed in uninjected oocyte pairs. These are hallmark features of highly adhesive cell:cell interfaces. Several point mutations in Po were engineered, corresponding to the molecular defects in the CMT type 1B or DSS. The proteins encoded by these mutations reached the cell surface but failed to concentrate at the oocyte interface. Po carrying a point mutation that is found in DSS is not targeted on the plasma membrane and fail to accumulate at the cell-cell contact site.     

Crustacean Hyperglycemic Hormone (cHH) as a Modulator of Aggression in Crustacean Decapods

Biogenic amines, particularly serotonin, are recognised to play an important role in controlling the aggression of invertebrates, whereas the effect of neurohormones is still underexplored. The crustacean Hyperglycemic Hormone (cHH) is a multifunctional member of the eyestalk neuropeptide family. We expect that this neuropeptide influences aggression either directly, by controlling its expression, or indirectly, by mobilizing the energetic stores needed for the increased activity of an animal. Our study aims at testing such an influence and the possible reversion of hierarchies in the red swamp crayfish, Procambarus clarkii, as a model organism. Three types of pairs of similarly sized males were formed: (1) ‘control pairs’ (CP, n = 8): both individuals were injected with a phosphate saline solution (PBS); (2) ‘reinforced pairs’ (RP, n = 9): the alpha alone was injected with native cHH, and the beta with PBS; (3) ‘inverted pairs’ (IP, n = 9): the opposite of (2). We found that, independently of the crayfish’s prior social experience, cHH injections induced (i) the expression of dominance behaviour, (ii) higher glycemic levels, and (iii) lower time spent motionless. In CP and RP, fight intensity decreased with the establishment of dominance. On the contrary, in IP, betas became increasingly likely to initiate and escalate fights and, consequently, increased their dominance till a temporary reversal of the hierarchy. Our results demonstrate, for the first time, that, similarly to serotonin, cHH enhances individual aggression, up to reverse, although transitorily, the hierarchical rank. New research perspectives are thus opened in our intriguing effort of understanding the role of cHH in the modulation of agonistic behaviour in crustaceans.     

Nutrigenomic Analysis of Diet-Gene Interactions on Functional Supplements for Weight Management

Recent advances in molecular biology combined with the wealth of information generated by the Human Genome Project have fostered the emergence of nutrigenomics, a new discipline in the field of nutritional research. Nutrigenomics may provide the strategies for the development of safe and effective dietary interventions against the obesity epidemic. According to the World Health Organization, more than 60% of the global disease burden will be attributed to chronic disorders associated with obesity by 2020. Meanwhile in the US, the prevalence of obesity has doubled in adults and tripled in children during the past three decades. In this regard, a number of natural dietary supplements and micronutrients have been studied for their potential in weight management. Among these supplements, (–)-hydroxycitric acid (HCA), a natural extract isolated from the dried fruit rind of Garcinia cambogia, and the micronutrient niacin-bound chromium(III) (NBC) have been shown to be safe and efficacious for weight loss. Utilizing cDNA microarrays, we demonstrated for the first time that HCA-supplementation altered the expression of genes involved in lipolytic and adipogenic pathways in adipocytes from obese women and up-regulated the expression of serotonin receptor gene in the abdominal fat of rats. Similarly, we showed that NBC-supplementation up-regulated the expression of myogenic genes while suppressed the expression of genes that are highly expressed in brown adipose tissue in diabetic obese mice. The potential biological mechanisms underlying the observed beneficial effects of these supplements as elucidated by the state-of-the-art nutrigenomic technologies will be systematically discussed in this review.Key Words: Insulin resistance, glucose tolerance factor, supplemental chromium, Garcinia cambogia, (-)-hydroxycitric acid, overweight, obesity, diabetes, cardiovascular disease, nutritional interventions, microarrays, nutrigenomics.     

Functional and Evolutionary Significance of Human MicroRNA Seed Region Mutations

MicroRNAs have emerged in recent years as important regulators of cell function in both normal and diseased cells. MiRNAs coordinately regulate large suites of target genes by mRNA degradation and/or translational inhibition. The mRNA target specificities of miRNAs in animals are primarily encoded within a 7 nt “seed region” mapping to positions 2–8 at the molecule''s 5′ end. We here combine computational analyses with experimental studies to explore the functional significance of sequence variation within the seed region of human miRNAs. The results indicate that a substitution of even a single nucleotide within the seed region changes the spectrum of mRNA targets by >50%. The high functional cost of even single nucleotide changes within seed regions is consistent with their high sequence conservation among miRNA families both within and between species and suggests processes that may underlie the evolution of miRNA regulatory control.     

In Silico Analysis of Crustacean Hyperglycemic Hormone Family

Through multiple sequence alignment and phylogenetic analysis, the subgrouping of the crustacean hyperglycemic hormone (CHH) family was updated using the most complete, nonredundant sequence data set. All sequences from insects were clustered into a distinct subbranch with characters closer to CHH subfamily I. Several sequences that are controversial in their nomenclature and classification are discussed. The motif configuration of CHHs differs from that of molt-inhibiting hormone or gonad-inhibiting hormone in both N and C termini. These two motifs approach each other in tertiary structure models, and the motif preference reveals the critical roles of these regions in functional specificity. Two types of exon organizations of the CHH family genes were observed. Four-exon Chh genes were found in a wide range of pan-crustacean (crustacean and hexapod) taxa, except for the penaeid species, from which the 3-exon Chh genes were reported. Meanwhile, the 3-exon structure was found in the Mih gene and Moih genes from one brachyuran species. Combining gene scan skill and exon splicing rules found in this study, we define three more novel sequences from two insect genomes. The pattern of the exon-exon junction within the mature peptide segment is preserved in all CHH family members.The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint first authors.     

Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts

Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic ‘arms races’ with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in ‘housekeeping’ functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts.     

Crustacean Neuromuscular Mechanisms: Functional Morphology of Nerve Terminals and the Mechanism of Facilitation

Two aspects of crustacean neuromuscular physiology are discussed:(1) the ultrastructural identification of the excitatory andinhibitory nerve terminals, and (2) the characteristics of,and the possible mechanisms for, facilitation. The first problem was studied in crayfish opener muscle whichhas one excitatory and one inhibitory axon. One of the nerveswas stimulated in the presence of DNP until synaptic transmissionfailed; the preparations were then fixed for electron microscopy.Whenever the excitatory nerve was stimulated, the terminalswith round synaptic vesicles were depleted while nearby terminalswith smaller elongate vesicles were normal. When the inhibitorynerve was stimulated, the converse was true. The possible reasons for the diversity in crustacean neuromuscularproperties are discussed. Large EPSP's with a high quantal content(m), appear to be produced by terminals which are invaded bya propagated spike. Small EPSP's (small m) appear to be producedby terminals which don't spike and which are depolarized bya decrementally conducted potential. There is an inverse relationshipbetween m and the amount of facilitation. The physiologicalbasis for facilitation is discussed; previous hypotheses arefound wanting and a new one is proposed, that of slow depolarization.     

Modulatory Interactions of Resting-State Brain Functional Connectivity

The functional brain connectivity studies are generally based on the synchronization of the resting-state functional magnetic resonance imaging (fMRI) signals. Functional connectivity measures usually assume a stable relationship over time; however, accumulating studies have reported time-varying properties of strength and spatial distribution of functional connectivity. The present study explored the modulation of functional connectivity between two regions by a third region using the physiophysiological interaction (PPI) technique. We first identified eight brain networks and two regions of interest (ROIs) representing each of the networks using a spatial independent component analysis. A voxel-wise analysis was conducted to identify regions that showed modulatory interactions (PPI) with the two ROIs of each network. Mostly, positive modulatory interactions were observed within regions involved in the same system. For example, the two regions of the dorsal attention network revealed modulatory interactions with the regions related to attention, while the two regions of the extrastriate network revealed modulatory interactions with the regions in the visual cortex. In contrast, the two regions of the default mode network (DMN) revealed negative modulatory interactions with the regions in the executive network, and vice versa, suggesting that the activities of one network may be associated with smaller within network connectivity of the competing network. These results validate the use of PPI analysis to study modulation of resting-state functional connectivity by a third region. The modulatory effects may provide a better understanding of complex brain functions.