bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single gene directs both production and immunity of halocin C8 in a haloarchaeal strain AS7092
Authors: Sun Chaomin , Li Yun , Mei Shuangshuang , Lu Qiuhe , Zhou Ligang , Xiang Hua 
Published: June 2005

SummaryHalocin C8 (HalC8) is an extremely stable and hydrophobic microhalocin with 76 amino acids, and has a wide inhibitory spectrum against the haloarchaea. It is derived from the C‐terminus of a 283‐amino‐acid prepro‐protein (ProC8), which was demonstrated by molecular cloning of the halC8 gene, and verified by the N‐terminal amino acid sequencing as well as MALDI‐TOF‐MS analysis of the purified HalC8. The production of this halocin is controlled through both transcription regulation and protein processing: the halC8 transcripts and HalC8 activity rapidly increased to maximal levels upon transition from exponential to stationary phase. However, while halC8 transcripts remained abundant, the HalC8 processing was inhibited during stationary phase. Remarkably, agar‐diffusion test revealed the unprocessed ProC8 and its 207‐amino‐acid N‐terminal peptide (HalI), with or without the putative Tat signal sequence, were capable to block the halocin activity of HalC8 in vitro. In addition, heterologous expression of HalI in Haloarcula hispanica rendered this sensitive strain remarkable resistance to HalC8, indicating that HalI encodes the immunity property of the producer. In accordance with this immunity function, HalI and ProC8 were both found localized on the cellular membrane. Protein interaction assay revealed that HalI likely sequestrated the HalC8 activity by specific binding. To our knowledge, this is the first report on halocin immunity, and our results that a single gene encodes both peptide antibiotic and immunity protein also provide a novel immune mechanism for peptide antibiotics.
Binding sites of VanRB and σ70 RNA polymerase in the vanB vancomycin resistance operon of Enterococcus faecium BM4524
Authors: Depardieu Florence , Courvalin Patrice , Kolb Annie 
Published: June 2005

SummaryThe vanB operon of Enterococcus faecium BM4524 which confers inducible resistance to vancomycin is composed of the vanRBSB gene encoding a two‐component regulatory system and the vanYBWHBBXB resistance genes that are transcribed from promoters PRB and PYB respectively. In this study, primer extension revealed transcription start sites at 13 and 48 bp upstream from the start codon of vanRB and vanYB, respectively, that allowed identification of −10 and −35 promoter motifs. The VanRB protein was overproduced in Escherichia coli, purified and phosphorylated (VanRB‐P) non‐enzymically with acetylphosphate. VanRB‐P and VanRB specifically bound to PRB and PYB promoters. VanRB bound at a single site at position −32.5 upstream from the PRB transcriptional start site and at two sites at positions −33.5 and −55.5 upstream from that of PYB. The proximal VanRB binding site overlapped the −35 region of both promoters. VanRB was converted from a monomer to a dimer upon acetylphosphate treatment. VanRB‐P had higher affinity than VanRB for its targets and appeared more efficient than VanRB in promoting open complex formation with PRB and PYB. In the absence of regulator, E. coli RNA polymerase was able to interact with PRB but not with PYB. Phosphorylation of VanRB significantly increased promoter interaction with RNA polymerase and led to an extended and modified footprint. In vitro transcription assays showed that VanRB‐P activates PYB more strongly than PRB. Analysis of the protected regions revealed one copy of a 21 bp sequence in the PRB promoter and two copies in the PYB promoter which may serve as recognition sites for VanRB and VanRB‐P binding that are required for transcriptional activation and expression of vancomycin resistance.
Cell cycle‐regulated degradation of tmRNA is controlled by RNase R and SmpB
Authors: Hong Sue‐Jean , Tran Quyen‐Anh , Keiler Kenneth C. 
Published: June 2005

SummaryThe  production  and  removal  of  regulatory  RNAs must be controlled to ensure proper physiological responses. SsrA RNA (tmRNA), a regulatory RNA conserved in all bacteria, is cell cycle regulated and is important for control of cell cycle progression in Caulobacter crescentus. We report that RNase R, a highly conserved 3′ to 5′ exoribonuclease, is required for the selective degradation of SsrA RNA in stalked cells. Purified RNase R degrades SsrA RNA in vitro, and is kinetically competent to account for all SsrA RNA turnover. SmpB, a tmRNA‐binding protein, protects SsrA RNA from RNase R degradation in vitro, and the levels of SmpB protein during the cell cycle correlate with SsrA RNA stability. These results suggest that SmpB binding controls the timing of SsrA RNA degradation by RNase R. We propose a model for the regulated degradation of SsrA RNA in which RNase R degrades SsrA RNA from a non‐tRNA‐like 3′ end, and SmpB specifically protects SsrA RNA from RNase R. This model explains the regulation of SsrA RNA in other bacteria, and suggests that a highly conserved regulatory mechanism controls SsrA activity.
The transcriptional activator ClgR controls transcription of genes involved in proteolysis and DNA repair in Corynebacterium glutamicum
Authors: Engels Sabine , Ludwig Carsten , Schweitzer Jens‐Eric , Mack Christina , Bott Michael , Schaffer Steffen 
Published: June 2005

SummaryExpression of the structural genes encoding the ATP‐dependent proteases ClpCP and Lon in Corynebacterium glutamicum and Streptomyces lividans is activated by the transcriptional regulator ClgR in response to yet unknown environmental stimuli. As it was not known whether ClgR controls expression of additional genes we used DNA microarrays in order to comprehensively define the ClgR regulon in C. glutamicum. The mRNA levels of 16 genes decreased ≥ 2‐fold in a ΔclgRΔclpC mutant (ClgR absent) compared with a ΔclpC mutant (ClgR present). For five genes in four operons (NCgl0748, ptrB, hflX and NCgl0240‐recR) regulation by ClgR could be independently verified by primer extension analyses and confirmation of binding of purified ClgR to the regulatory regions of these operons. ptrB encodes an endopeptidase, which is consistent with the proteolytic functions of the genes already known to be under ClgR control. However, RecR is unrelated to proteolysis but required for recombinational repair of UV‐induced DNA damage. Possibly ClgR‐dependent activation of gene expression is triggered by environmental stresses damaging both proteins and nucleic acids, although DNA damage induced by UV radiation and mitomycin C treatment did not result in ClgR‐dependent transcriptional activation of any of the newly identified ClgR regulon members. In order to functionally analyse the NCgl0748 and hflX genes we have constructed C. glutamicum strains with deletions in these genes. The ΔNCgl0748 mutant displayed reduced growth rates in minimal and rich media. The NCgl0748 protein was shown to be localized in the cytoplasm only, while the HflX pool is equally distributed between cytoplasm and plasma membrane. In order to study the proposed degradation of ClgR by ClpCP we have constructed a conditional clpP1P2 mutant. Depletion of ClpP1 and ClpP2 in that strain resulted in the accumulation of ClgR, indicating that ClgR is in fact a substrate of the ClpCP1 and/or ClpCP2 protease in C. glutamicum.
Contributions of protein structure and gene position to the compartmentalization of the regulatory proteins σE and SpoIIE in sporulating Bacillus subtilis
Authors: McBride Shonna M. , Rubio Aileen , Wang Lei , Haldenwang William G. 
Published: June 2005

SummaryAt an early stage in endospore formation Bacillus subtilis partitions itself into two dissimilar compartments with unique developmental fates. Transcription appropriate to each compartment is initiated by the activation of compartment‐specific RNA polymerase sigma subunits, σE in the mother cell and σF in the forespore. Among the possible factors contributing to the compartment specificity of σE and σF is the selective accumulation of the σE protein in the mother cell and that of SpoIIE, a regulatory phosphatase essential to the activation of σF, in the forespore. In the current work, fluorescent microscopy is used to investigate the contributions of σE and SpoIIE's protein structures, expression and the genetic asymmetry that develops during chromosome translocation into the forespore on their abundance in each compartment. Time of entry of the spoIIE and sigE genes into the forespore was found to have a significant effect on the enrichment of their products in one or the other compartment. In contrast, the structures of the proteins themselves do not appear to promote their transfer to a particular compartment, but nonetheless contribute to compartmentalization by facilitating degradation in the compartment where each protein's activity would be inappropriate.
Cells lacking ClpB display a prolonged shutoff phase of the heat shock response in Caulobacter crescentus
Authors: Simão Rita C. G. , Susin Michelle F. , Alvarez‐Martinez Cristina E. , Gomes Suely L. 
Published: June 2005

SummaryThe heat shock response in Caulobacter crescentus was previously shown to be positively regulated by the alternative sigma factor of RNA polymerase (RNAP) σ32, and negatively modulated by DnaK during the induction phase of the heat shock response but not during the recovery phase. In the present work we have investigated the involvement of the chaperone ClpB in the control of the heat shock response in C. crescentus. Data obtained indicated a role of ClpB in downregulation of heat shock protein (HSP) synthesis, as cells lacking this chaperone showed a prolonged shutoff phase of the heat shock response. In Escherichia coli, it has been proposed that the DnaK chaperone system switches transcription back to constitutively expressed genes through simultaneous reactivation of heat‐aggregated σ70, as well as sequestration of σ32 away from RNAP. In C. crescentus, results obtained with a clpB null mutant indicate that ClpB could be involved in the reactivation of the major sigma factor σ73. In support of this hypothesis, we showed that transcription directed from σ73‐dependent promoters is not switched back in the clpB null mutant during the recovery phase. Furthermore, we observed that resolubilization of heat‐aggregated σ73 is dependent on the presence of ClpB. Our findings also indicated that the absence of ClpB made cells more sensitive to heat shock and ethanol but not to other stresses, and unable to acquire thermotolerance.
Nursing Synchronization and Milk Ejection Failure as Maternal Strategies to Reduce Allosuckling in Pair‐Housed Sows (Sus scrofa domestica)
Authors: Illmann Gudrun , Pokorná Zuzana , Špinka Marek 
Published: June 2005

AbstractNon‐offspring nursing (allosuckling) is costly for lactating females. It is reasonable to assume, therefore, that mechanisms have evolved to control the frequency of allosuckling. It is suggested that the synchronization of nursing between females could be such a mechanism. The aim of this study was to investigate whether nursing synchronization is related to the timing of nursing behaviour of paired sows and the behaviour of alien piglets in relation to allosuckling. Specifically, we predicted that: (i) nursing synchronization will increase if there is a real risk of allosuckling compared with a situation where there is none, (ii) nursing synchronization indeed reduces allosuckling and, therefore, those nursings with allosuckling attempts will be less closely synchronized than those without allosuckling attempts and (iii) in non‐synchronized nursings, the sows will more often employ another strategy to reduce allosuckling, namely, they will make the nursings non‐nutritive by not releasing milk. Ten pairs of sows and their litters were used in this study. For each pair, the two sows were housed individually until their litters were weaned; however, their litters had access to both sows from day 11 post‐partum. The behaviour of the 10 pairs of sows with their litters was videotaped for 6 h on days 10, 11, 17 and 24 post‐partum. The frequency of allosuckling attempts, non‐nutritive nursings and allosuckling during milk ejection was analysed for every pair for every day of observation. The observed frequency of nursing synchronization was high. The median interval between the start of a nursing within one pair of sows was 32 s. The first prediction was supported as synchronization became significantly tighter when piglets were given the possibility to allosuckle on day 11 [Cochran–Mantel–Haenszel (CMH) statistics, p < 0.0001]. The second prediction was also supported; the nursings were less closely synchronized when there were allosuckling attempts (CMH statistics, p < 0.05). Of all nursings, 36% had an allosuckling attempt; however, only 17% resulted in real allosuckling. Evidence in favour of the third prediction was also found as non‐nutritive nursings were more frequent in non‐synchronized nursings (CMH statistics, p < 0.05). Finally, real allosuckling during milk ejection was unrelated to the degree of nursing synchronization, as in less synchronized nursings, the sows responded to allosuckling attempts by not releasing milk. Our results suggest that sows are not able to completely suppress allosuckling; however, they can reduce its frequency through nursing synchronization and non‐nutritive nursings.
German Yellowjacket (Vespula germanica) Foragers Use Odors Inside the Nest to Find Carbohydrate Food Sources
Authors: Jandt Jennifer M. , Jeanne Robert L. 
Published: June 2005

AbstractPrior work has shown that yellowjacket waSPS remember food odors and use them as cues when foraging. There is also evidence they have mechanisms to recruit nest mates to highly rewarding food sources, as naïve individuals are more likely to go to food sources with scents similar to those visited by nest mates. We asked whether recruitment requires behavioral stimulation by returning foragers, as in honey bees, or if sampling the food source inside the nest is sufficient. We tested this by eliminating the behavior of returning foragers by inserting a scented sugar solution directly into a Vespula germanica nest. Exiting foragers were given a choice of the test scent and a control scent. WaSPS were more likely to choose the test scent. We conclude that behavioral interactions with returning foragers are not necessary to stimulate nest mates to associate an odor with a food source and search for a resource bearing that odor, and that experience with the scented reward inside the nest is sufficient to achieve this result.
Is Male Cohabitation Costly for Females of the Spider Stegodyphus lineatus (Eresidae)?
Authors: Erez Tamar , Schneider Jutta M. , Lubin Yael 
Published: June 2005

AbstractReproductive interests of females and males can vary over a number of issues, including the number of matings and the occurrence and duration of mate guarding and cohabitation. The mating system of the spider Stegodyphus lineatus (Eresidae) is characterized by an exceptional sexual conflict where males induce females to remate by committing infanticide. Females experience high costs because of this male strategy, while males benefit. During the mating season, males tend to stay with females for several days. We examined whether this male strategy of cohabitation is also disadvantageous for females of S. lineatus. A field experiment revealed that male presence in a female's nest negatively affected her body condition, whereas cohabiting males gained weight because they fed on prey caught in webs of females. As a response, females did not renew their webs when males were present. Thus, females with a cohabiting male experienced the combined cost of prey loss and loss of time available for foraging. These costs are expected to increase with every additional cohabiting male. Mated females behaved more aggressively toward males than did virgin females. This behavior may be interpreted as an adaptive response to reduce mating costs.
Time Learning and Anticipatory Activity in Groups of Arctic Charr
Authors: Brännäs Eva , Berglund Ulf , Eriksson Lars‐Ove 
Published: June 2005

AbstractTime learning and anticipatory activity were studied in five groups of 16–17 Arctic charr (Salvelinus alpinus) using self‐feeding devices with individual recognition (PIT (Passive Integrated Transponders)‐tags). The fish were kept under a LD 12:12 h cycle and periods of free access to the food were alternated with periods of time‐limited (2 h) access to food. Self‐feeding activity was significantly related to the light period in unrestricted conditions while related to the feeding periods during time‐limited access to food. The fish learned to concentrate their feeding activity to the restricted mealtime (>50% of the daily self‐feeding activity) within 10 d. The food anticipatory activity, measured as an increased self‐feeding activity before the feeding time and as aggressive interactions close to the trigger, was significant in both cases. The dominant individuals increased the trigger activity in advance of the time‐restricted reward period and subdominant individuals approached the trigger also in advance, inducing aggressive interactions. Thus, anticipating and learning a temporally predictable food source was pronounced in groups of self‐feeding Arctic charr.
Formation of an Olfactory Search Image for Explosives Odours in Sniffer Dogs*
Authors: Gazit Irit , Goldblatt Allen , Terkel Joseph 
Published: June 2005

AbstractThe term ‘search image’ refers to an animal's heightened ability to detect a specific cryptic prey, after experience with that prey. Formulated in 1960 by Tinbergen (Archives Neerlandaises de zoologie, vol. 13, pp. 265–343), the search image concept has been the subject of much research, albeit almost entirely based on visual search cues in birds of prey. Given the theoretical and practical importance of this concept for foraging or searching in general, we set out to investigate whether dogs could form olfactory search images for explosive odours. Seven experienced explosives detector dogs were first tested for their ability to detect 30 g of the explosives 2,4,6‐trinitrotoluene (TNT), RDX + polyisobutylene + di(2‐ethylhexyl)sebacate + fuel oil (C4) or pentaerythritol tetranitrate (PETN) placed in various containers randomly distributed along a 300‐m limestone track. In consecutive stages of the experiment, we altered the relative percentages of the three explosives. The results showed that the percentage of TNT containers detected by the dogs increased in trials that followed placing of a high percentage of TNT relative to other explosives and decreased in trials that follwed placing of a relatively low percentage of TNT containers. The percentage detection of C4 and PETN was not influenced by their relative abundance at any stage. Overall, these results suggest that dogs can form an olfactory search image that might aid in prey/target detection.
Learning in realistic networks of spiking neurons and spike‐driven plastic synapses
Authors: Mongillo Gianluigi , Curti Emanuele , Romani Sandro , Amit Daniel J. 
Published: June 2005

AbstractWe have used simulations to study the learning dynamics of an autonomous, biologically realistic recurrent network of spiking neurons connected via plastic synapses, subjected to a stream of stimulus–delay trials, in which one of a set of stimuli is presented followed by a delay. Long‐term plasticity, produced by the neural activity experienced during training, structures the network and endows it with active (working) memory, i.e. enhanced, selective delay activity for every stimulus in the training set. Short‐term plasticity produces transient synaptic depression. Each stimulus used in training excites a selective subset of neurons in the network, and stimuli can share neurons (overlapping stimuli). Long‐term plasticity dynamics are driven by presynaptic spikes and coincident postsynaptic depolarization; stability is ensured by a refresh mechanism. In the absence of stimulation, the acquired synaptic structure persists for a very long time. The dependence of long‐term plasticity dynamics on the characteristics of the stimulus response (average emission rates, time course and synchronization), and on the single‐cell emission statistics (coefficient of variation) is studied. The study clarifies the specific roles of short‐term synaptic depression, NMDA receptors, stimulus representation overlaps, selective stimulation of inhibition, and spike asynchrony during stimulation. Patterns of network spiking activity before, during and after training reproduce most of the in vivo physiological observations in the literature.
Neuronal mechanisms underlying control of a brain–computer interface
Authors: Hinterberger Thilo , Veit Ralf , Wilhelm Barbara , Weiskopf Nikolaus , Vatine Jean‐Jacques , Birbaumer Niels 
Published: June 2005

AbstractBrain–computer interfaces (BCIs) enable humans or animals to communicate or control external devices without muscle activity using electric brain signals. The BCI used here is based on self‐regulation of slow cortical potentials (SCPs), a skill that most people and paralyzed patients can acquire with training periods of several hours up to months. The neurophysiological mechanisms and anatomical sources of SCPs and other event‐related brain potentials have been described but the neural mechanisms underlying the self‐regulation skill for the use of a BCI are unknown. To uncover the relevant areas of brain activation during regulation of SCPs, the BCI was combined with functional magnetic resonance imaging. The electroencephalogram was recorded inside the magnetic resonance imaging scanner in 12 healthy participants who learned to regulate their SCP with feedback and reinforcement. The results demonstrate activation of specific brain areas during execution of the brain regulation skill allowing a person to activate an external device; a successful positive SCP shift compared with a negative shift was closely related to an increase of the blood oxygen level‐dependent response in the basal ganglia. Successful negativity was related to an increased blood oxygen level‐dependent response in the thalamus compared with successful positivity. These results may indicate learned regulation of a cortico‐striatal‐thalamic loop modulating local excitation thresholds of cortical assemblies. The data support the assumption that human subjects learn the regulation of cortical excitation thresholds of large neuronal assemblies as a prerequisite for direct brain communication using an SCP‐driven BCI. This skill depends critically on an intact and flexible interaction between the cortico‐basal ganglia‐thalamic circuits.