bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control of the cell elongation–division cycle by shuttling of PBP1 protein in Bacillus subtilis
Authors: Claessen Dennis , Emmins Robyn , Hamoen Leendert W. , Daniel Richard A. , Errington Jeff , Edwards David H. 
Published: March 2008

SummaryThe characteristic shape of bacterial cells is mainly determined by the cell wall, the synthesis of which is orchestrated by penicillin‐binding proteins (PBPs). Rod‐shaped bacteria have two distinct modes of cell wall synthesis, involved in cell elongation and cell division, which are believed to employ different sets of PBPs. A long‐held question has been how these different modes of growth are co‐ordinated in space and time. We have now identified the cell division protein, EzrA, and a newly discovered protein, GpsB, as key players in the elongation–division cycle of Bacillus subtilis. Mutations in these genes have a synthetic phenotype with defects in both cell division and cell elongation. They also have an unusual bulging phenotype apparently due to a failure in properly completing cell pole maturation. We show that these phenotypes are tightly associated with disturbed localization of the major transglycosylase/transpeptidase of the cell, PBP1. EzrA and GpsB have partially differentiated roles in the localization cycle of PBP1, with EzrA mainly promoting the recruitment of PBP1 to division sites, and GpsB facilitating its removal from the cell pole, after the completion of pole maturation.
The metabolic activity of Mycobacterium tuberculosis, assessed by use of a novel inducible GFP expression system, correlates with its capacity to inhibit phagosomal maturation and acidification in human macrophages
Authors: Lee Bai‐Yu , Clemens Daniel L. , Horwitz Marcus A. 
Published: March 2008

Summary Mycobacterium tuberculosis generally reside in phagosomes within human macrophages that resist maturation and acidification, but exhibit significant heterogeneity. In this study we have constructed an IPTG‐inducible GFP expression system in M. tuberculosis to assess the relationship between the metabolic status of M. tuberculosis and the degree of phagosomal maturation. Using these recombinant bacteria, we have found that, in human macrophages, M. tuberculosis that respond to IPTG with expression of GFP fluorescence, and hence are metabolically active, reside in non‐acidified phagosomes that have not fused with Texas red dextran pre‐labelled lysosomes. In contrast, M. tuberculosis that fail to express GFP in response to IPTG, and hence are metabolically inactive, reside within acidified phagosomes that have fused with Texas red dextran labelled lysosomes. These studies demonstrate that metabolic activity of M. tuberculosis correlates strongly with phagosomal maturation and that the inducible GFP expression system is useful for assessing metabolic activity of intracellular M. tuberculosis.
Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1‐interacting protein CUL4
Authors: Wang Songhu , Liu Jikai , Feng Yuanyuan , Niu Xiangli , Giovannoni Jim , Liu Yongsheng 
Published: March 2008

SummaryFruits are a major source of nutrition in human diets, providing carbohydrates, fiber, vitamins and phytonutrients. Carotenoids are a principal class of compounds found in many fruits, providing nutritional benefits both as precursors to essential vitamins and as antioxidants. Molecular characterization revealed that the tomato high pigment mutant genes (hp1 and hp2) encode UV‐DAMAGED DNA BINDING PROTEIN‐1 (DDB1) and DE‐ETIOLATED‐1 (DET1) homologs, respectively, and both are essential components of the recently identified CUL4‐based E3 ligase complex. Here we have isolated a tomato CUL4 homolog and performed yeast two‐hybrid assays to suggest possible association of tomato DDB1 with CUL4 and DET1. Real‐time RT‐PCR analysis indicated that both HP1 and CUL4 are expressed constitutively. Abscisic acid is implicated in plastid division control and its application substantially enhances HP1/DDB1 mRNA accumulation. Transformation of constructs expressing CUL4–YFP and DDB1–YFP fusion proteins driven by the CaMV 35S promoter reveals that both CUL4 and DDB1 are targeted to tomato plastids and nuclei simultaneously. Using fruit‐specific promoters combined with RNAi technology, we show that downregulated DDB1 expression in transgenic fruits results in a significant increase in the number of plastids and corresponding enhanced pigment accumulation. CUL4‐RNAi repression lines provide insight regarding CUL4 function during tomato development, and reveal that this tomato cullin is important in the regulation of plastid number and pigmentation, which in turn have a direct impact on fruit nutrient quality.
DNA‐binding specificity, transcriptional activation potential, and the rin mutation effect for the tomato fruit‐ripening regulator RIN
Authors: Ito Yasuhiro , Kitagawa Mamiko , Ihashi Nao , Yabe Kimiko , Kimbara Junji , Yasuda Junichi , Ito Hirotaka , Inakuma Takahiro , Hiroi Seiji , Kasumi Takafumi 
Published: March 2008

SummaryThe RIN gene encodes a putative MADS box transcription factor that controls tomato fruit ripening, and its ripening inhibitor (rin) mutation yields non‐ripening fruit. In this study, the molecular properties of RIN and the rin mutant protein were clarified. The results revealed that the RIN protein accumulates in ripening fruit specifically and is localized in the nucleus of the cell. In vitro studies revealed that RIN forms a stable homodimer that binds to MADS domain‐specific DNA sites. Analysis of binding site selection experiments revealed that the consensus binding sites of RIN highly resemble those of the SEPALLATA (SEP) proteins, which are Arabidopsis MADS box proteins that control the identity of floral organs. RIN exhibited a transcription‐activating function similar to that exhibited by the SEP proteins. These results indicate that RIN exhibits similar molecular functions to SEP proteins although they play distinctly different biological roles. In vivo assays revealed that RIN binds to the cis‐element of LeACS2. Our results also revealed that the rin mutant protein accumulates in the mutant fruit and exhibits a DNA‐binding activity similar to that exhibited by the wild‐type protein, but has lost its transcription‐activating function, which in turn would inhibit ripening in mutant fruit.
A membrane‐bound NAC transcription factor NTL8 regulates gibberellic acid‐mediated salt signaling in Arabidopsis seed germination
Authors: Kim Sang‐Gyu , Lee An‐Kyo , Yoon Hye‐Kyung , Park Chung‐Mo 
Published: March 2008

SummaryGibberellic acid (GA) plays a key role in seed germination through coordinate interactions with other growth hormones and external signals. However, the way in which external signals are incorporated into the GA‐signaling pathway is largely unknown. Here, we demonstrate that a membrane‐bound NAC transcription factor NTL8 mediates the salt regulation of seed germination via the GA pathway, primarily independently of ABA. NTL8 is induced by high salinity. Its expression is also elevated by a GA biosynthetic inhibitor paclabutrazol (PAC), but is repressed by GA. Notably, high salinity greatly represses the GA3 oxidase 1 (GA3ox1) gene, supporting the hypothesis that salt signals inhibit seed germination by repressing GA biosynthesis. Induction of NTL8 and repression of GA3ox1 by high salinity still occur in the ABA‐deficient aba3‐1 mutant. Accordingly, the germination of a T‐DNA insertional ntl8‐1 mutant seed is resistant to high salinity and PAC. Interestingly, NTL8 is significantly induced during cold imbibition, but the induction declines quickly in germinating seeds, like RGL2. NTL8 activity is also regulated by controlled proteolytic release of the membrane‐bound NTL8 form. Its release from the membranes is activated by PAC and high salinity. Our data support that NTL8 modulates GA‐mediated salt signaling in regulating seed germination. This regulatory scheme may provide an adaptative fitness, which delays seed germination under high salinity conditions.
Ethylene regulates lateral root formation and auxin transport in Arabidopsis thaliana
Authors: Negi Sangeeta , Ivanchenko Maria G. , Muday Gloria K. 
Published: March 2008

SummaryLateral root branching is a genetically defined and environmentally regulated process. Auxin is required for lateral root formation, and mutants that are altered in auxin synthesis, transport or signaling often have lateral root defects. Crosstalk between auxin and ethylene in root elongation has been demonstrated, but interactions between these hormones in the regulation of Arabidopsis lateral root formation are not well characterized. This study utilized Arabidopsis mutants altered in ethylene signaling and synthesis to explore the role of ethylene in lateral root formation. We find that enhanced ethylene synthesis or signaling, through the eto1‐1 and ctr1‐1 mutations, or through the application of 1‐aminocyclopropane‐1‐carboxylic acid (ACC), negatively impacts lateral root formation, and is reversible by treatment with the ethylene antagonist, silver nitrate. In contrast, mutations that block ethylene responses, etr1‐3 and ein2‐5, enhance root formation and render it insensitive to the effect of ACC, even though these mutants have reduced root elongation at high ACC doses. ACC treatments or the eto1‐1 mutation significantly enhance radiolabeled indole‐3‐acetic acid (IAA) transport in both the acropetal and the basipetal directions. ein2‐5 and etr1‐3 have less acropetal IAA transport, and transport is no longer regulated by ACC. DR5‐GUS reporter expression is also altered by ACC treatment, which is consistent with transport differences. The aux1‐7 mutant, which has a defect in an IAA influx protein, is insensitive to the ethylene inhibition of root formation. aux1‐7 also has ACC‐insensitive acropetal and basipetal IAA transport, as well as altered DR5‐GUS expression, which is consistent with ethylene altering AUX1‐mediated IAA uptake, and thereby blocking lateral root formation.
Combined use of phenotypic and genotypic information in sampling animals for genotyping in detection of quantitative trait loci
Authors: Ansari‐Mahyari S. , Berg P. 
Published: March 2008

SummaryConventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half‐sib families and 120 daughters per family. The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL was significantly higher for both MinERR and MaxLRT compared with EP and random genotyping methods (either across or within family), for all the proportions of genotyped animals. Power to detect significant QTL (α = 0.01) with 20% genotyping for MinERR and MaxLRT was 80 and 75% of that obtained with complete genotyping compared with 70 and 38% genotyping for EP within and across families respectively. With 30% genotyping, the powers were 78, 83, 78 and 58% respectively. The estimated variance components were unbiased in EP strategies (within and across family), only when at least 30% was genotyped. To decrease the number of genotyped individuals either MinERR or MaxLRT could be considered. With 20% genotyping in MinERR, the estimated QTL variance components were not significant compared with complete genotype information but all studied strategies at 20% genotyping overestimated the QTL effect. Results showed that combining the phenotypic and genotypic information in selective genotyping (e.g. MinERR and MaxLRT) is better than using only the EPs and the combined methods can be considered as alternative approaches to decrease genotyping costs, with unbiased QTL effects, decreased sampling variance of the QTL variance component and also increased the power of QTL detection.
Comparison of models for genetic evaluation of survival traits in dairy cattle: a simulation study
Authors: Jamrozik J. , Fatehi J. , Schaeffer L.R. 
Published: March 2008

SummaryThree models for the analysis of functional survival data in dairy cattle were compared using stochastic simulation. The simulated phenotype for survival was defined as a month after the first calving (from 1 to 100) in which a cow was involuntarily removed from the herd. Parameters for simulation were based on survival data of the Canadian Jersey population. Three different levels of heritability of survival (0.100, 0.050 and 0.025) and two levels of numbers of females per generation (2000 or 4000) were considered in the simulation. Twenty generations of random mating and selection (on a second trait, uncorrelated with survival) with 20 replicates were simulated for each scenario. Sires were evaluated for survival of their daughters by three models: proportional hazard (PH), linear multiple‐trait (MT), and random regression (RR) animal models. Different models gave different ranking of sires with respect to survival of their daughters. Correlations between true and estimated breeding values for survival to five different points in a cow’s lifetime after the first calving (120 and 240 days in milk after first, second, third and fourth calving) favoured the PH model, followed by the RR model evaluations. Rankings of models were independent of the heritability level, female population size and sire progeny group size (20 or 100). The RR model, however, showed a slight superiority over MT and PH models in predicting the proportion of sire’s daughters that survived to the five different end‐points after the first calving.
Neural encoding of auditory temporal context in a songbird basal ganglia nucleus, and its independence of birds' song experience
Authors: Kojima Satoshi , Doupe Allison J. 
Published: March 2008

AbstractSome of the most complex auditory neurons known are found in the songbird forebrain, throughout the ‘song system’, including its basal ganglia nucleus Area X. These cells are selective for the temporal order of the bird's own song (BOS): they typically respond strongly to BOS, but more weakly when the syllable sequence of BOS is played in reverse order (roBOS), indicating that they integrate auditory information over more than single syllables. Here, studying the zebra finch Area X, we found that order selectivity strongly depends on the mean syllable duration of individual songs, decreasing markedly as this duration approaches 150–200 ms. Simply segmenting the same songs differently, creating an increase in average syllable length towards 150 ms, caused a similar decrease in order selectivity. This suggests that song neurons integrate acoustic information over a relatively limited time window, predominantly less than 150 ms. We provided further support for this by showing that a significant fraction of Area X order selectivity was accounted for by the acoustic similarity between each BOS and roBOS, measured using cross‐correlation with fixed window sizes, but only when the correlation windows were at least 50 ms and no more than 200 ms long. All the same findings were evident in birds raised without tutor exposure, indicating that tutor learning has little effect on neural mechanisms underlying song temporal selectivity. Our results suggest that song‐selective neurons encode much of the temporal context of song using a short, constant time window that is conserved across differences in songs, birds and learning.
Postsynaptic µ‐opioid receptor response in the median preoptic nucleus is altered by a systemic sodium challenge in rats
Authors: Henry Mélaine , Drolet Guy , Mouginot Didier 
Published: March 2008

AbstractThe median preoptic nucleus (MnPO) is an integrator site for the chemosensory and neural signals induced by a perturbation in the hydromineral balance, and it is highly involved in controlling fluid and electrolyte ingestion. Here, we hypothesize that opioid peptides, previously recognized to control ingestive behaviors, may regulate the excitability of MnPO neurons and that this regulatory action may depend on the natriuric (Na+) status of body fluid compartments. Our results show that activation of µ‐, but not δ‐, opioid receptors (OR) triggered a membrane hyperpolarization by recruiting a G‐protein‐regulated inward‐rectifier K+ (GIRK) conductance in 41% of the neurons tested. Interestingly, 24 h Na+ depletion strengthened this opioid‐mediated control of neuronal excitability. In Na+‐depleted animals, the neuronal population displaying the µ‐OR‐induced hyperpolarization expanded to 60% (Z‐test, P = 0.012), whereas Na+ repletion restored this population to the control level (39%; Z‐test, P = 0.037). Among the neurons displaying µ‐OR‐induced hyperpolarization, Na+ depletion specifically increased the neuronal population responsive to variation in ambient Na+ (from 27% to 43%; Z‐test, P = 0.029). In contrast, Na+ repletion dramatically reduced the population that was unresponsive to Na+ (from 17% to 3%; Z‐test, P = 0.031). Neither the basic properties of the neurons nor the characteristics of the µ‐OR‐induced response were altered by the body Na+ challenge. Our results indicate that an episode of Na+ depletion/Na+ repletion modifies the organization of the opioid‐sensitive network of the MnPO. Such network plasticity might be related to the avid salt ingestion triggered by repeated Na+ depletion.
The spatio‐temporal and subcellular expression of the candidate Down syndrome gene Mnb/Dyrk1A in the developing mouse brain suggests distinct sequential roles in neuronal development
Authors: Hämmerle Barbara , Elizalde Carina , Tejedor Francisco J. 
Published: March 2008

AbstractIt is widely accepted that the neurological alterations in Down syndrome (DS) are principally due to modifications in developmental processes. Accordingly, a large part of the research on DS in recent years has focused on chromosome 21 genes that influence brain development. MNB/DYRK1A is one of the genes on human chromosome 21 that has raised most interest, due to its relationship with the brain functions that are altered in DS. Although a number of interesting experimental mouse models for DS are being developed, we still know little about the expression of Mnb/Dyrk1A during mouse brain development. Here, we report that Mnb/Dyrk1A displays a rather dynamic spatio‐temporal expression pattern during mouse central nervous system development. Our data indicate that Mnb/Dyrk1A is specifically expressed in four sequential developmental phases: transient expression in preneurogenic progenitors, cell cycle‐regulated expression in neurogenic progenitors, transient expression in recently born neurones, and persistent expression in late differentiating neurones. Our results also suggest that the subcellular localization of MNB/DYRK1A, including its translocation to the nucleus, is finely regulated. Thus, the MNB/DYRK1A protein kinase could be a key element in the molecular machinery that couples sequential events in neuronal development. This rich repertoire of potential functions in the developing central nervous system is suitable to be linked to the neurological alterations in DS through the use of mouse experimental models.
Matrix metalloproteinases MMP2 and MMP9 are upregulated by noradrenaline in the mouse neuroendocrine hypothalamus
Authors: Maolood N. , Hardin‐Pouzet H. , Grange‐Messent V. 
Published: March 2008

AbstractMagnocellular neurons of the hypothalamic supraoptic nuclei (SON) are involved in the synthesis and release of two major neuropeptides: oxytocin (OT) and arginine‐vassopressin (AVP). Neurochemical plasticity in this system is induced by physiological conditions such as lactation, parturition and dehydration, and may be accompanied by reversible structural plasticity affecting neurons, astrocytes and the extracellular matrix (ECM). The noradrenergic system plays a critical role in triggering this chemical plasticity associated with structural plasticity. Matrix metalloproteinases (MMPs) are good candidates for involvement in the ECM remodelling observed in structural plasticity. We investigated the possible regulation of the two gelatinases, MMP2 and MMP9, by noradrenaline (NA) in the mouse neuroendocrine hypothalamus. We looked for the presence, location and activity of MMP2 and MMP9 in the SON, using anex vivoexperimental model of mouse hypothalamic slices incubated for 4 h with 10−4 mNA. We showed that: (i) immunoreactivity for MMP2 and MMP9 was detected not only in AVP‐positive and OT‐positive magnocellular neurons, but also in astrocyte processes in control and NA‐treated slices; (ii) the number of MMP2‐ and MMP9‐positive cells increased after incubation with NA; (iii) MMP2 and MMP9 displayed markedly higher levels of gelatinolytic activity after NA treatment. These results suggest that both MMP2 and MMP9 are regulated by NA, and could therefore also be involved in structural plasticity within the SON.
Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles
Authors: Takacs‐Vesbach Cristina , Mitchell Kendra , Jackson‐Weaver Olan , Reysenbach Anna‐Louise 
Published: March 2008

SummaryIt has been suggested that the distribution of microorganisms should be cosmopolitan because of their enormous capacity for dispersal. However, recent studies have revealed that geographically isolated microbial populations do exist. Geographic distance as a barrier to dispersal is most often invoked to explain these distributions. Here we show that unique and diverse sequences of the bacterial genus Sulfurihydrogenibium exist in Yellowstone thermal springs, indicating that these sites are geographically isolated. Although there was no correlation with geographic distance or the associated geochemistry of the springs, there was a strong historical signal. We found that the Yellowstone calderas, remnants of prehistoric volcanic eruptions, delineate biogeographical provinces for the Sulfurihydrogenibium within Yellowstone (χ2: 9.7, P = 0.002). The pattern of distribution that we have detected suggests that major geological events in the past 2 million years explain more of the variation in sequence diversity in this system than do contemporary factors such as habitat or geographic distance. These findings highlight the importance of historical legacies in determining contemporary microbial distributions and suggest that the same factors that determine the biogeography of macroorganisms are also evident among bacteria.