Distant informational interactions in bacteria

Exchange of information between bacteria via physical signals, referred to as "distant interactions" (DI), is the subject of this review. All cases of DI reported to date are discussed, as well as the history of these studies and the place of DI in bacterial communication. Bacterial DI are a particular case of DI occurring in nature (in plants, animals, and fungi). Along with the chemical signals of intracellular communications, DI play a significant role in the life of microorganisms, especially during critical periods.     

Defective Interfering Influenza Virus RNAs: Time To Reevaluate Their Clinical Potential as Broad-Spectrum Antivirals?

Defective interfering (DI) RNAs are highly deleted forms of the infectious genome that are made by most families of RNA viruses. DI RNAs retain replication and packaging signals, are synthesized preferentially over infectious genomes, and are packaged as DI virus particles which can be transmitted to susceptible cells. Their ability to interfere with the replication of infectious virus in cell culture and their potential as antivirals in the clinic have long been known. However, until now, no realistic formulation has been described. In this review, we consider the early evidence of antiviral activity by DI viruses and, using the example of DI influenza A virus, outline developments that have led to the production of a cloned DI RNA that is highly active in preclinical studies not only against different subtypes of influenza A virus but also against heterologous respiratory viruses. These data suggest the timeliness of reassessing the potential of DI viruses as a novel class of antivirals that may have general applicability.     

Extreme ends of the genome are conserved and rearranged in the defective interfering RNAs of semliki forest virus

We have analyzed Semliki Forest virus defective interfering RNA molecules, generated by serial undiluted passaging of the virus in baby hamster kidney cells. The 42 S RNA genome (about 13 kb ²) has been greatly deleted to generate the DI RNAs, which are heterogeneous both in size (about 2 kb) and sequence content. The DI RNAs offer a system for exploring binding sites for RNA polymerase and encapsidation signals, which must have been conserved in them since they are replicated and packaged. In order to study the structural organization of DI RNAs, and to analyze which regions from the genome have been conserved, we have determined the nucleotide sequences of (1) a 2.3 kb long DI RNA molecule, DI309, (2) 3′-terminal sequences (each about 0.3 kb) of two other DI RNAs, and (3) the nucleotide sequence of 0.4 kb at the extreme 5′ end of the 42 S RNA genome.The DI309 molecule consists of a duplicated region with flanking unique terminal sequences. A 273-nucleotide sequence is present in four copies per molecule. The extreme 5′-terminal nucleotide sequence of the 42 S RNA genome is shown to contain domains that are conserved in the two DI RNAs of known structure: DI309, and the previously sequenced DI301 (Lehtovaara et al., 1981). Here we report which terminal genome sequences are conserved in the DI RNAs, and how they have been modified, rearranged or amplified.     

Down-regulation of photosystem 2 efficiency and spectral reflectance in mango leaves under very low irradiance and varied chilling treatments

In order to elucidate the effects of chilling-stress at night on photosystem 2 (PS2) efficiency under dim irradiance (DI), mango leaves were chilled to varied extent (8–3 °C) and for varied duration (0–12 h) in growth cabinets in the dark, and then exposed to DI (20 μmol m⁻² s⁻¹ PPFD) at each chilling-temperature for 1 h. Chilling in the dark had little effect on F_v/F_m of mango leaves. But both the extent and duration of chilling pre-treatments significantly affected F_v’/F_m’ when leaves were exposed to DI. This down-regulation of PS2 efficiency was closely related to xanthophyll de-epoxidation, assessed as photochemical reflectance index (PRI) and calculated from leaf spectral reflectance [(R₅₃₁ − R₅₇₀)/(R₅₃₁ + R₅₇₀)], and non-photochemical quenching (NPQ). The down-regulation of PS2 is a defence mechanism initiated at predawn in winter to alleviate the damage of PS2 by the sudden and strong irradiation at sunrise. Mango leaves, transferred suddenly from warm and dark room to DI and chilling showed a slight down-regulation of PS2 efficiency, in spite of an increased xanthophyll de-epoxidation. This might have been due to the unavailability of some cofactors required for NPQ.     

Fundamental and applied objectives of investigation in dry immersion

The results of extended comparative research in the effect of hypogravity on the motor system in space flights and ground-based experiments have shown that “dry” immersion (DI) is the most adequate model of microgravity—the time of development, and the volume and depth of structural and functional motor disorders in DI are very close to what is observed in real microgravity. The high intensity and speed of development of hypogravity effects during immersion hypokinesia in comparison with bed rest hypokinesia, differing from DI only by the level of support deafferentation, promoted an insight into the leading (triggering) role of support lessness in the genesis of microgravity-induced syndromes of muscular deconditioning and hypogravitational ataxia. The involvement and pathways of support afferentation within the muscular system were experimentally studied and verified. The mechanisms of the development of changes in the activity of the system mechanisms remain much less investigated. These issues, as well as some new approaches for the elimination of the negative effects of hypogravity, were the subjects of investigation in the program of a complex dry immersion experiment, the results of which are presented in this issue of the journal.     

The AU-rich RNA recombination hot spot sequence of Brome mosaic virus is functional in tombusviruses: implications for the mechanism of RNA recombination

RNA recombination can be facilitated by recombination signals present in viral RNAs. Among such signals are short sequences with high AU contents that constitute recombination hot spots in Brome mosaic virus (BMV) and retroviruses. In this paper, we demonstrate that a defective interfering (DI) RNA, a model template associated with Tomato bushy stunt virus (TBSV), a tombusvirus, undergoes frequent recombination in plants and protoplast cells when it carries the AU-rich hot spot sequence from BMV. Similar to the situation with BMV, most of the recombination junction sites in the DI RNA recombinants were found within the AU-rich region. However, unlike BMV or retroviruses, where recombination usually occurred with precision between duplicated AU-rich sequences, the majority of TBSV DI RNA recombinants were imprecise. In addition, only one copy of the AU-rich sequence was essential to promote recombination in the DI RNA. The selection of junction sites was also influenced by a putative cis-acting element present in the DI RNA. We found that this RNA sequence bound to the TBSV replicase proteins more efficiently than did control nonviral sequences, suggesting that it might be involved in replicase "landing" during the template switching events. In summary, evidence is presented that a tombusvirus can use the recombination signal of BMV. This supports the idea that common AU-rich recombination signals might promote interviral recombination between unrelated viruses.     

Cell culture-based production of defective interfering particles for influenza antiviral therapy

Defective interfering particles (DIPs) lack an essential portion of the virus genome, but retain signals for replication and packaging, and therefore, interfere with standard virus (STV) replication. Due to this property, DIPs can be potential antivirals. The influenza A virus DIP DI244, generated during propagation in chicken eggs, has been previously described as a potential candidate for influenza antiviral therapy. As a cell culture-based manufacturing process would be more suitable to fulfill large-scale production needs of an antiviral and enables full process control in closed systems, we investigated options to produce DI244 in the avian cell line AGE1.CR.pIX in chemically defined suspension culture. With a DI244 fraction of 55.8% compared to STV, the highest DI244 yield obtained from 50 million cells was 4.6 × 10⁹ vRNA copies/mL at 12 h post infection. However, other defective genomes were also detected. Since these additionally produced defective particles are non-infectious, they might be still useful in antiviral therapies. In case they would interfere with quality of the final product, we examined the impact of virus seeds and selected process parameters on DI244 yield and contamination level with other defective particles. With a DI244 fraction of 5.5%, the yield obtained was 1.7 × 10⁸ vRNA copies/mL but now without additional defective genomes. Although the DI244 yield might be decreased in this case, such controlled manufacturing conditions are not available in chicken eggs. Overall, the application of these findings can support design and optimization of a cell culture-based production process for DIPs to be used as antivirals.

     

Cloning and characterization of the <Emphasis Type="Italic">Tne</Emphasis>DI restriction–modification system of <Emphasis Type="Italic">Thermotoga neapolitana</Emphasis>

A putative Type II restriction–modification system of Thermotoga neapolitana, TneDI, was cloned into Escherichia coli XL1-Blue MRF′ and characterized. Gene CTN_0339 specifies the endonuclease R.TneDI, while CTN_0340 encodes the cognate DNA methyltransferase M.TneDI. Both enzymes were purified simply by heating the cell lysates of E. coli followed by centrifugation. The enzymes were active over a broad range of temperatures, from 42°C to at least 77°C, with the highest activities observed at 77°C. R.TneDI cleaved at the center of the recognition sequence (CG↓CG) and generated blunt-end cuts. Overexpression of R.TneDI in BL21(DE3) was confirmed by both SDS-PAGE and Western blotting.     

Analysis of the interdependence of temperament, neuroendocrine control, and psychophysiological state during dry immersion

The interdependence of temperament and the hormonal and psychophysiological states was investigated in eight young volunteers during seven-day dry immersion (DI). The levels of insulin and sex, steroid, and thyroid hormones in the blood and the psychomotor parameters were determined on days 3 and 7 of DI and on day 7 of recovery. Before DI, the volunteers filled in Cattell’s personality questionnaire. During DI, anxious subjects spent less time to compare visual patterns, demonstrating a stably high speed of reactions with a slight quality loss. Extraverts showed a high speed of reactions and stability of psychomotor parameters without an increase in the number of errors. Easy-tempered and introvert subjects retained inherently high insulin concentrations in DI. Support deprivation was accompanied by the drop of the triiodothyronine and cortisol levels and an increase in prolactin and thyroxin. The results of multiple correlation analysis led to the conclusion that DI emphasizes the role of original extra-introversion and dampers the original anxiety. Success can be attained by adequate alteration of the levels of steroid and thyroid hormones with effectively balanced vagoinsulin—sympathoadrenal neuroendocrine control and monoaminergic CNS activity.     

The scabrous protein can act as an extracellular antagonist of notch signaling in the Drosophila wing

Notch (N) is a receptor for signals that inhibit neural precursor specification [1-6]. As N and its ligand Delta (DI) are expressed homogeneously, other molecules may be differentially expressed or active to permit neural precursor cells to arise intermingled with nonneural cells [7,8]. During Drosophila wing development, the glycosyltransferase encoded by the gene fringe (fng) promotes N signaling in response to DI, but inhibits N signaling in response to Serrate (Ser), which encodes a ligand that is structurally similar to DI. Dorsal expression of Fng protein localizes N signaling to the dorsoventral (DV) wing margin [9-11]. The secreted protein Scabrous (Sca) is a candidate for modulation of N in neural cells. Mutations at the scabrous (sca) locus alter the locations where precursor cells form in the peripheral nervous system [12,13]. Unlike fringe, sca mutations act cell non-autonomously [12]. Here, we report that targeted misexpression of Sca during wing development inhibited N signaling, blocking expression of all N target genes. Sca reduced N activation in response to DI more than in response to Ser. Ligand-independent signaling by overexpression of N protein, or by expression of activated truncated N molecules, was not inhibited by Sca. Our results indicate that Sca can act on N to reduce its availability for paracrine and autocrine interactions with DI and Ser, and can act as an antagonist of N signaling.     

Dynamics of hematologic parameters and of the erythrocyte deformability index at the juvenal period of rats and guinea pigs

In experiments on Wistar rats and guinea pigs, dynamics of blood hematological parameters and of erythrocyte deformability index (DI) was studied from birth to the 3-month age. In rats, significant changes were revealed in the picture of blood for the first month of postnatal ontogenesis. The number of erythrocytes and leukocytes sharply increased, the number of reticulocytes decreased, their ratio in the degree of maturity was changed. The mean erythrocyte volume and their acidic resistance also decreased. Prior to the 4-week age, DI increased, which was accompanied by an increase in the hemoglobin hydration and flattening of the erythrocyte shape. Then DI decreased and erythrocytes acquired the more spherical shape. After the critical period of 3–4 weeks the studied parameters reached plateau. In guinea pigs, at this period of ontogenesis the hematologic parameters had sufficiently stable values, except for a DI decrease from birth to 1.5 months, then it rose without reaching the initial values. Like in the case with rats, DI had a close correlation with the erythrocyte parameter of shape (O_min).     

Analysis of interdependence of temperament,neuroendocrine control and psychophysiological state during dry immersion

Interdependence of temperament, hormonal and psychophysiological states was investigated in eight young volunteers during seven-day dry immersion (DI). The levels of insulin and sex, steroid, and thyroid hormones in the blood and the psychomotor parameters were determined on days 3 and 7 of DI and on day 7 of recovery. Before DI, the volunteers filled in the Cattell’s Personality Factor Questionnaire. During DI, anxious subjects spent less time to compare visual patterns, demonstrating a high and stable speed of reactions with a slight deterioration. Extraverts showed high speed of reactions and stability of psychomotor parameters without increase in the number of errors. Easy-tempered and introvert subjects preserved inherently high insulin concentrations in DI. Support deprivation was accompanied by the drop of triiodothyronine and cortisol levels and the increase in prolactin and thyroxin. The results of multiple correlation analysis lead to the conclusion that DI increased the role of original extra-introversion and decreased that of the original anxiety. Successful activity can be attained by adequate alteration of the levels of steroid and thyroid hormones with effectively balanced vagoinsular-sympathoadrenal neuroendocrine control and monoaminergic CNS activity.     

MDA5 participates in the detection of paramyxovirus infection and is essential for the early activation of dendritic cells in response to Sendai Virus defective interfering particles

Defective interfering (DI) particles are byproducts of virus replication that potently enhance dendritic cell (DC) maturation by virus infection. DI particles have been reported for many different viruses and are strong inducers of type I IFNs. The cellular mechanisms involved in the response to DI particles are not known. In this study, we show that 1) DI particles are recognized by more than one viral sensor independently of TLRs and type I IFN signaling; 2) The helicase MDA5 participates in the detection of DI genomes as MDA5-deficient DCs respond inefficiently to Sendai virus stocks containing DI particles; 3) DI particles stimulate the expression of IRF3-responsive genes by a uniquely potent mechanism when compared with other prototypic viral stimulus; and 4) the efficient detection of DI particles overcomes virus immune antagonism. These data highlight the outstanding adjuvant capacity of DI particles in stimulating mouse and human DCs. They also offer biological relevance to the previously reported inhibition of MDA5 by different paramyxovirus V proteins. The unique mechanism by which DI particles trigger the maturation of DCs represents a novel strategy that could be further exploited for the development of potent adjuvant molecules.     

The normal distribution as appropriate model of developmental instability in Opuntia cacti flowers

Developmental instability (DI) as measured by fluctuating asymmetry (FA) has been proposed to reflect fitness and stress. Furthermore, the associated developmental buffering may reduce morphological variation, conceal the expression of genetic variation and as such play an important role in evolutionary biology. However, observed associations between FA and various forms of stress and quality appear very heterogeneous. Presently it is difficult to interpret the biological relevance of this heterogeneity because little is known about the link between FA and the underlying process of DI, casting doubt whether DI can be viewed as an individual property and how closely FA reflects the underlying process of DI. Therefore, studies that explicitly test the validity of assumptions of the proposed theoretical models and estimate between‐individual variations in DI are needed. We present data on Opuntia cacti floral traits confirming that the normal distribution can be viewed as an appropriate approximation of the distribution of DI and that the concept of hypothetical repeatability can provide useful insights into the interpretation of patterns in FA as a measure of DI. Furthermore, we detected significant between‐individual variation in DI. Measuring petals from several flowers within individual plants allowed making inference of individual DI.     

Between‐family variation and quantitative genetics of developmental instability of long bones in rabbit foetuses

The genetic basis of developmental instability (DI) remains largely unknown as a result of its morphological expression, fluctuating asymmetry (FA), poorly reflecting DI, especially if few traits are studied. The typically low values of heritability of FA (h²_FA) can be translated into higher values of DI (h²_DI) by the hypothetical repeatability, yet leading to wide confidence intervals. Thus, high sample sizes and/or several traits are indispensible for reaching meaningful conclusions. To obtain more insights into quantitative genetic variation of DI, we investigated between‐family variance in DI in six long bones of 1126 foetuses of the New Zealand white rabbit from a full‐sib experiment. We applied different approaches to obtain genetic parameters for DI. Heritabilities and the coefficients of between‐family variation (CVB) were calculated for six individual traits and composite indices. The results obtained, despite a likely upward bias as a result of maternal and non‐additive effects, lend support to the presence of moderate additive genetic variance for DI. It is suggested that, in foetal traits, the environmental variance was minimal, leading to a high likelihood of detecting genetic variation in DI, thus creating an ideal model system for studying the genetic basis of DI. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 33–42.     

Defective interfering particles of poliovirus: mapping of the deletion and evidence that the deletions in the genomes of DI(1), (2) and (3) are located in the same region.

The deletions in RNAs of three defective interfering (DI) particles of poliovirus type 1 have been located and their approximate extent determined by three methods. (1) Digestion with RNase III of DI RNAs yields the same 3′-terminal fragments as digestion with RNase III of standard virus RNA. The longest 3′-terminal fragment has a molecular weight of 1.55 × 10⁶. This suggests that the deletions are located in the 5′-terminal half of the polio genome. (2) Fingerprints of RNase T₁-resistant oligonucleotides of all three DI RNAs are identical and lack four large oligonucleotides as compared to the fingerprints of standard virus, an observation suggesting that the deletions in all three DI RNAs are located in the same region of the viral genome. The deletion-specific oligonucleotides have also been shown to be within the 5′-terminal half of the viral genome by alkali fragmentation of the RNA and fingerprinting poly (A)-linked (3′-terminal) fragments of decreasing size. (3) Virion RNA of DI(2) particles was annealed with denatured double-stranded RNA (RF) of standard virus and the hybrid heteroduplex molecules examined in the electron microscope. A single loop, approximately 900 nucleotides long and 20% from one end of the molecules, was observed. Both the size and extent of individual deletions is somewhat variable in different heteroduplex molecules, an observation suggesting heterogeneity in the size of the deletion in RNA of the DI(2) population. Our data show that the DI RNAs of poliovirus contain an internal deletion in that region of the viral genome known to specify the capsid polypeptides. This result provides an explanation as to why poliovirus DI particles are unable to synthesize viral coat proteins.     

Deletion mapping of a mouse hepatitis virus defective interfering RNA reveals the requirement of an internal and discontiguous sequence for replication.

All of the defective interfering (DI) RNAs of mouse hepatitis virus (MHV) contain both the 5' and 3' ends of the viral genomic RNA, which presumably include the cis sequences required for RNA replication. To define the replication signal of MHV RNA, we have used a vaccinia virus-T7 polymerase-transcribed MHV DI RNA to study the effects of sequence deletion on DI RNA replication. Following infection of susceptible cells with a recombinant vaccinia virus expressing T7 RNA polymerase, various cDNA clones derived from a DI RNA (DIssF) of the JHM strain of MHV, which is a 3.5-kb naturally occurring DI RNA, behind a T7 promoter were transfected. On superinfection with a helper MHV, the ability of various DI RNAs to replicate was determined. Serial deletions from the middle of the RNA toward both the 5' and 3' ends demonstrated that 859 nucleotides from the 5' end and 436 nucleotides from the 3' end of the MHV RNA genome were necessary for RNA replication. Surprisingly, an additional stretch of 135 nucleotides located at 3.1 to 3.3 kb from the 5' end of the genome was also required. This stretch is discontiguous from the 5'-end cis replication signal and is present in all of the naturally occurring DI RNAs studied so far. The requirement for a long stretch of 5'- and 3'-end sequences predicts that the subgenomic MHV mRNAs cannot replicate. The efficiency of RNA replication varied with different cDNA constructs, suggesting possible interaction between different regions of DI RNA. The identification of MHV RNA replication signals allowed the construction of an MHV DI-based expression vector, which can express foreign genes, such as the chloramphenicol acetyltransferase gene.     

Macro-alga population shows low but significant heterogeneity in developmental instability with no detectable association with individual fitness

We studied among-individual variation in developmental instability (DI) and fitness-related parameters in 80 individual plants of Fucus vesiculosus (Phaeophyta). To minimize differential environmental effects, plants were sampled from one environmentally homogenous population. DI was measured as fluctuating asymmetry (FA) of four bilaterally symmetric traits (branch length, receptacle length and width, and bladder width) for an average total of 30 structures per individual. FA levels varied significantly among individual plants, consistent with a coefficient of variation of 0.12 for organism-wide DI or 0.13–0.21 for trait-specific DI. These values are lower than estimates for other organisms, suggesting that the genetic heterogeneity in DI was low. The data provide some evidence for organism-wide DI, but simulations show that organism-wide and trait-specific variation cannot be conclusively separated. Growth rate of branch tips was determined experimentally, demonstrating significant variation among individuals. FA was not significantly correlated with growth rate or with morphological variables associated with fecundity, age, size, and health. At the same time, the signs of all the correlation coefficients were consistent with the expectation of a negative relationship between DI and fitness. The simulations indicated that the correlation between FA and the underlying DI was comparatively strong (high hypothetical repeatability), implying that the lack of significant associations between FA and fitness variables reflected a weak relationship between DI and these fitness parameters. This weak relationship may be related to the low amount of DI variation in the study population.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 277–286.     

Relevance of nonlinear lumped-parameter models in the analysis of depth-EEG epileptic signals

In the field of epilepsy, the analysis of stereoelectroencephalographic (SEEG, intra-cerebral recording) signals with signal processing methods can help to better identify the epileptogenic zone, the area of the brain responsible for triggering seizures, and to better understand its organization. In order to evaluate these methods and to physiologically interpret the results they provide, we developed a model able to produce EEG signals from “organized” networks of neural populations. Starting from a neurophysiologically relevant model initially proposed by Lopes Da Silva et al. [Lopes da Silva FH, Hoek A, Smith H, Zetterberg LH (1974) Kybernetic 15: 27–37] and recently re-designed by Jansen et al. [Jansen BH, Zouridakis G, Brandt ME (1993) Biol Cybern 68: 275–283] the present study demonstrates that this model can be extended to generate spontaneous EEG signals from multiple coupled neural populations. Model parameters related to excitation, inhibition and coupling are then altered to produce epileptiform EEG signals. Results show that the qualitative behavior of the model is realistic; simulated signals resemble those recorded from different brain structures for both interictal and ictal activities. Possible exploitation of simulations in signal processing is illustrated through one example; statistical couplings between both simulated signals and real SEEG signals are estimated using nonlinear regression. Results are compared and show that, through the model, real SEEG signals can be interpreted with the aid of signal processing methods. Received: 3 January 2000 / Accepted: 24 March 2000     

Developmental instability, hybridization and heterozygosity in stick insects of the genus Bacillus (Insecta; Phasmatodea) with different modes of reproduction

Several genetic factors are assumed to influence developmental instability (DI). One is the level of heterozygosity, with higher levels often being associated with decreased DI; another is genetic incompatibility in hybrids, which in several cases has been shown to increase DI. The genus Bacillus includes species which have both amphigonic heterozygous reproducing populations and homozygous parthenogenetic reproducing populations (B. rossius rossius and B. r. redtenbacheri). Furthermore, Bacillus includes hybrid parthenogenetic species, which have very high levels of almost fixed heterozygosities (B. atticus, B. whitei, B. lynceorum). We investigated the phenotypic variance (σ²p) and the impact of hybridization and level of heterozygosity on DI in females from these populations and species of Bacillus. DI was estimated as fluctuating asymmetry (FA) for three bilateral traits: the labial palpus, the maxillary palpus and the antenna. For the labial palpus and maxillary palpus we found, in general, a lower level of DI in the amphigonic females compared with parthenogenetic counterparts from the same species and with parthenogenetic females from the three hybrid species. A higher DI of the antenna was found in the hybrid species when compared with both parthenogenetic and amphigonic populations of the nonhybrid species, suggesting that the genes controlling antenna development are located on the sex chromosomes. The development of the investigated bilateral characters in the hybrid species seemed to be affected more by factors relating to genetic incompatibilities as a consequence of hybridization than by the stabilizing force of increased heterozygosity. Only few differences in σ²p were observed, supporting the possibility that the observed differences in DI are related mainly to internal genetic factors. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 249–259.