bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rrp1, a cyclic‐di‐GMP‐producing response regulator, is an important regulator of Borrelia burgdorferi core cellular functions
Authors: Rogers Elizabeth A. , Terekhova Darya , Zhang Hong‐Ming , Hovis Kelley M. , Schwartz Ira , Marconi Richard T. 
Published: February 2009

SummaryTwo‐component systems (TCS) are universal among bacteria and play critical roles in gene regulation. Our understanding of the contributions of TCS in the biology of the Borrelia is just now beginning to develop. Borrelia burgdorferi, a causative agent of Lyme disease, harbours a TCS comprised of open reading frames (ORFs) BB0419 and BB0420. BB0419 encodes a response regulator designated Rrp1, and BB0420 encodes a hybrid histidine kinase–response regulator designated Hpk1. Rrp1, which contains a conserved GGDEF domain, undergoes phosphorylation and produces the secondary messenger, cyclic diguanylate (c‐di‐GMP), a critical signaling molecule in numerous organisms. However, the regulatory role of the Rrp1–Hpk1 TCS and c‐di‐GMP signaling in Borrelia biology are unexplored. In this study, the distribution, conservation, expression and potential global regulatory capability of Rrp1 were assessed. rrp1 was found to be universal and highly conserved among isolates, co‐transcribed with hpk1, constitutively expressed during in vitro cultivation, and significantly upregulated upon tick feeding. Allelic exchange replacement and microarray analyses revealed that the Rrp1 regulon consists of a large number of genes encoded by the core Borrelia genome (linear chromosome, linear plasmid 54 and circular plasmid 26) that encode for proteins involved in central metabolic processes and virulence mechanisms including immune evasion.
Fc‐receptors and immunity to malaria: from models to vaccines
Authors: PLEASS R. J. 
Published: February 2009

SUMMARY The complexity and number of antigens (Ags) seen during an immune response has hampered the development of malaria vaccines. Antibodies (Abs) play an important role in immunity to malaria and their passive administration is effective at controlling the disease. Abs represent approximately 25% of all proteins undergoing clinical trials, and these ‘smart biologicals’ have undergone a major revival with the realization that Abs lie at the interface between innate and adaptive immunity. At least 18 Abs have FDA approval for clinical use and approximately 150 are in clinical trials, the majority for the treatment of cancer, allograft rejection or autoimmune disease. Despite these triumphs none are in development for malaria, principally because they are perceived as being too expensive for a disease mainly afflicting poor and marginalized populations. Although unlikely, at least in the foreseeable future, that Ab‐based prophylaxis will be made available to the millions of people at risk from malaria, they may be incorporated into current vaccine approaches, since Abs act as correlates of protection in studies aimed at defining the best Ags to include in vaccines. Abs may also form the basis for novel vaccination strategies by targeting Ags to appropriate antigen presenting cells. Therefore, to develop the most efficacious vaccines it will be necessary to fully understand which Abs and Fc‐receptors (FcRs) are best engaged for a positive outcome.
A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature
Authors: Strasser Bárbara , Alvarez Mariano J. , Califano Andrea , Cerdán Pablo D. 
Published: February 2009

SummaryPlants regulate their time to flowering by gathering information from the environment. Photoperiod and temperature are among the most important environmental variables. Sub‐optimal, but not near‐freezing, temperatures regulate flowering through the thermosensory pathway, which overlaps with the autonomous pathway. Here we show that ambient temperature regulates flowering by two genetically distinguishable pathways, one requiring TFL1 and another requiring ELF3. The delay in flowering time observed at lower temperatures was partially suppressed in single elf3 and tfl1 mutants, whereas double elf3 tfl1 mutants were insensitive to temperature. tfl1 mutations abolished the temperature response in cryptochrome mutants that are deficient in photoperiod perception, but not in phyB mutants, which have a constitutive photoperiodic response. In contrast to tfl1, elf3 mutations were able to suppress the temperature response in phyB mutants, but not in cryptochrome mutants. Gene expression profiles revealed that the tfl1 and elf3 effects are due to the activation of different sets of genes, and identified CCA1 and SOC1/AGL20 as being important cross‐talk points. Finally, genome‐wide gene expression analysis strongly suggests a general and complementary role for ELF3 and TFL1 in temperature signalling.
CIPK6, a CBL‐interacting protein kinase is required for development and salt tolerance in plants
Authors: Tripathi Vineeta , Parasuraman Boominathan , Laxmi Ashverya , Chattopadhyay Debasis 
Published: February 2009

SummaryCalcineurin B‐like proteins (CBL) and CBL‐interacting protein kinases (CIPK) mediate plant responses to a variety of external stresses. Here we report that Arabidopsis CIPK6 is also required for the growth and development of plants. Phenotype of tobacco plants ectopically expressing a homologous gene (CaCIPK6) from the leguminous plant chickpea (Cicer arietinum) indicated its functional conservation. A lesion inAtCIPK6 significantly reduced shoot‐to‐root and root basipetal auxin transport, and the plants exhibited developmental defects such as fused cotyledons, swollen hypocotyls and compromised lateral root formation, in conjunction with reduced expression of a number of genes involved in auxin transport and abiotic stress response. The Arabidopsis mutant was more sensitive to salt stress compared to wild‐type, while overexpression of a constitutively active mutant of CaCIPK6 promoted salt tolerance in transgenic tobacco. Furthermore, tobacco seedlings expressing the constitutively active mutant of CaCIPK6 showed a developed root system, increased basipetal auxin transport and hypersensitivity to auxin. Our results provide evidence for involvement of a CIPK in auxin transport and consequently in root development, as well as in the salt‐stress response, by regulating the expression of genes.
Early production of thymic stromal lymphopoietin precedes infiltration of dendritic cells expressing its receptor in allergen‐induced late phase cutaneous responses in atopic subjects
Authors: Corrigan C. J. , Jayaratnam A. , Wang Y. , Liu Y. , De Waal Malefyt R. , Meng Q. , Kay A. B. , Phipps S. , Lee T. H. , Ying S. 
Published: February 2009

Background:  Thymic stromal lymphopoietin (TSLP) is an interleukin (IL)‐7‐like cytokine that triggers dendritic cell‐mediated T helper (Th)2 inflammatory responses through a receptor consisting of a heterodimer of the IL‐7 receptor alpha (IL‐7Rα) chain and the TSLP receptor (TSLPR), which resembles the cytokine receptor common gamma chain. Dendritic cells activated by TSLP prime development of CD4+ T cells into Th2 cells contributing to the pathogenesis of allergic inflammation. We hypothesized that allergen exposure induces expression of TSLP and results in recruitment of TSLPR bearing cells in the cutaneous allergen‐induced late‐phase reaction (LPR) in atopic subjects.Methods:  Skin biopsies were obtained from atopic subjects (n = 9) at various times after cutaneous allergen challenge. In situ hybridization and immunohistochemistry were used to determine TSLP mRNA expression and to measure infiltration of TSLPR+ DC in skin LPR. RT‐PCR and flow cytometry were employed to analyse TSLPR expression on isolated blood DC.Results:  Allergen‐induced skin TSLP expression occurred as early as 1 h after allergen challenge, whereas TSLPR+ and CD11c+ cells infiltrated relatively late (24–48 h). The majority of TSLPR+ cells were DC co‐expressing blood DC antigen‐1 (BDCA‐1) or BDCA‐2. Freshly isolated blood DC expressed both TSLPR and IL‐7Rα chains. Maturation and stimulation with TSLP or polyriboinosinic–polyribocytidylic acid in vitro upregulated the expression of both TSLPR and IL‐7Rα chains in DC but not in chemoattractant receptor‐homologous molecule expressed on Th2 cells+ CD4+ T cells.Conclusion:  The data suggest that TSLP plays a role in augmenting, through DC recruitment and activation, the development of Th2‐type T cells in allergic inflammation.
Genetic diversity of Swiss sheep breeds in the focus of conservation research
Authors: Glowatzki‐Mullis M.‐L. , Muntwyler J. , Bäumle E. , Gaillard C. 
Published: February 2009

SummaryThere is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long‐term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty‐one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour‐joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between‐breed variation ranged from −12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within‐breed diversity the removal of a breed could also produce an increase in diversity (−0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations.
Identifiability of parameters and behaviour of MCMC chains: a case study using the reaction norm model
Authors: Shariati M.M. , Korsgaard I.R. , Sorensen D. 
Published: February 2009

SummaryMarkov chain Monte Carlo (MCMC) enables fitting complex hierarchical models that may adequately reflect the process of data generation. Some of these models may contain more parameters than can be uniquely inferred from the distribution of the data, causing non‐identifiability. The reaction norm model with unknown covariates (RNUC) is a model in which unknown environmental effects can be inferred jointly with the remaining parameters. The problem of identifiability of parameters at the level of the likelihood and the associated behaviour of MCMC chains were discussed using the RNUC as an example. It was shown theoretically that when environmental effects (covariates) are considered as random effects, estimable functions of the fixed effects, (co)variance components and genetic effects are identifiable as well as the environmental effects. When the environmental effects are treated as fixed and there are other fixed factors in the model, the contrasts involving environmental effects, the variance of environmental sensitivities (genetic slopes) and the residual variance are the only identifiable parameters. These different identifiability scenarios were generated by changing the formulation of the model and the structure of the data and the models were then implemented via MCMC. The output of MCMC sampling schemes was interpreted in the light of the theoretical findings. The erratic behaviour of the MCMC chains was shown to be associated with identifiability problems in the likelihood, despite propriety of posterior distributions, achieved by arbitrarily chosen uniform (bounded) priors. In some cases, very long chains were needed before the pattern of behaviour of the chain may signal the existence of problems. The paper serves as a warning concerning the implementation of complex models where identifiability problems can be difficult to detect a priori. We conclude that it would be good practice to experiment with a proposed model and to understand its features before embarking on a full MCMC implementation.
Biology and host specificity of Aulacobaris fallax (Coleoptera: Curculionidae), a potential biological control agent for dyer’s woad, Isatis tinctoria (Brassicaceae) in North America
Authors: Gerber E. , Cortat G. , Hinz H. L. 
Published: February 2009

AbstractDyer’s woad, Isatis tinctoria, a plant of Eurasian origin is a problematic weed in western North America against which a classical biological weed control programme was initiated in 2004. Three European insect species were selected as candidate agents to control this invasive species, including the root‐mining weevil Aulacobaris fallax. To determine its suitability as an agent, the biology and host specificity of A. fallax were studied in outdoor plots and in the field between 2004 and 2006 in its native European range. Aulacobaris fallax is a univoltine species that lays its eggs from March to August into leaf stalks and roots of dyer’s woad. Larvae mine and pupate in the roots and adults emerge from August to October. Up to 62% of the dyer’s woad plants at the field sites investigated were attacked by this weevil. In no‐choice host‐specificity tests, A. fallax attacked 16 out of 39 species and varieties within the Family Brassicaceae. Twelve of these are native to North America. In subsequent multiple‐choice tests, seven species, all native to North America, suffered a similar level of attack as dyer’s woad, while none of the European species were attacked. Our results demonstrate the importance of including test plant species that have not co‐evolved with the respective candidate agent. In sum, we conclude that the risk of non‐target effects is too high for A. fallax to be considered as a biological control agent for dyer’s woad in the United States.
Are the palms Washingtonia filifera and Chamaerops humilis suitable hosts for the red palm weevil, Rhynchophorus ferrugineus (Col. Curculionidae)?
Authors: Dembilio Ó. , Jacas J. A. , Llácer E. 
Published: February 2009

AbstractThe red palm weevil, Rhynchophorus ferrugineus (Olivier) (Coleoptera, Curculionidae), is a widely distributed pest which has recently become the major pest of palms in the Mediterranean Basin. This weevil has been recorded on 19 different palm species, however, the host status of Washingtonia filifera and Chamaerops humilis remains unclear. The present study was carried out to check whether these species had either antixenotic or antibiotic mechanisms of resistance against this pest. Our results show that both W. filifera and C. humilis are resistant to R. ferrugineus. Resistance in W. filifera is based on antibiosis whereas in C. humilis resistance is based on antixenosis.
Differential maturation of circadian rhythms in clock gene proteins in the suprachiasmatic nucleus and the pars tuberalis during mouse ontogeny
Authors: Ansari Nariman , Agathagelidis Manuel , Lee Choogon , Korf Horst‐Werner , Von Gall Charlotte 
Published: February 2009

AbstractCircadian rhythms of many body functions in mammals are controlled by a master pacemaker, residing in the hypothalamic suprachiasmatic nucleus (SCN), which synchronises peripheral oscillators. The SCN and peripheral oscillators share several components of the molecular clockwork and comprise transcriptional activators (BMAL1 and CLOCK/NPAS2) and inhibitors (mPER1/2 and mCRY1/2). Here we compared the ontogenetic maturation of the clockwork in the SCN and pars tuberalis (PT). The PT is a peripheral oscillator that strongly depends on rhythmic melatonin signals. Immunoreactions for clock gene proteins were determined in the SCN and PT at four different timepoints during four differential stages of mouse ontogeny: foetal (embryonic day 18), newborn (2‐day‐old), infantile (10‐day‐old), and adult. In the foetal SCN, levels of immunoreactions of all clock proteins were significantly lower than adult levels except for BMAL1. In the newborn SCN the clock protein immunoreactions had not yet reached adult levels, but the infantile SCN showed similar levels of immunoreactions as the adult. In contrast, immunoreactions for all clock gene proteins in the foetal PT were as intense as in newborn, infantile and adult, and showed the same phase. As the foetal pineal gland is not yet capable of rhythmic melatonin production, the rhythms in clock gene proteins in the foetal PT are presumably dependent on the maternal melatonin signal. Thus, our data provide the first evidence that maternal melatonin is important for establishing and maintaining circadian rhythms in a foetal peripheral oscillator.
Musical experience and neural efficiency – effects of training on subcortical processing of vocal expressions of emotion
Authors: Strait Dana L. , Kraus Nina , Skoe Erika , Ashley Richard 
Published: February 2009

AbstractMusicians exhibit enhanced perception of emotion in speech, although the biological foundations for this advantage remain unconfirmed. In order to gain a better understanding for the influences of musical experience on neural processing of emotionally salient sounds, we recorded brainstem potentials to affective human vocal sounds. Musicians showed enhanced time‐domain response magnitude to the most spectrally complex portion of the stimulus and decreased magnitude to the more periodic, less complex portion. Enhanced phase‐locking to stimulus periodicity was likewise seen in musicians’ responses to the complex portion. These results suggest that auditory expertise engenders both enhancement and efficiency of subcortical neural responses that are intricately connected with acoustic features important for the communication of emotional states. Our findings provide the first biological evidence for behavioral observations indicating that musical training enhances the perception of vocally expressed emotion in addition to establishing a subcortical role in the auditory processing of emotional cues.
Soil CO2flux and photoautotrophic community composition in high‐elevation, ‘barren’ soil
Authors: Freeman Kristen R. , Pescador Monte Y. , Reed Sasha C. , Costello Elizabeth K. , Robeson Michael S. , Schmidt Steven K. 
Published: February 2009

SummarySoil‐dominated ecosystems, with little or no plant cover (i.e. deserts, polar regions, high‐elevation areas and zones of glacial retreat), are often described as ‘barren’, despite their potential to host photoautotrophic microbial communities. In high‐elevation, subnival zone soil (i.e. elevations higher than the zone of continuous vegetation), the structure and function of these photoautotrophic microbial communities remains essentially unknown. We measured soil CO2flux at three sites (above 3600 m) and used molecular techniques to determine the composition and distribution of soil photoautotrophs in the Colorado Front Range. Soil CO2flux data from 2002 and 2007 indicate that light‐driven CO2uptake occurred on most dates. A diverse community ofCyanobacteria,Chloroflexiand eukaryotic algae was present in the top 2 cm of the soil, whereas these clades were nearly absent in deeper soils (2–4 cm). Cyanobacterial communities were composed of lineages most closely related toMicrocoleus vaginatusandPhormidium murrayi, eukaryotic photoautotrophs were dominated by green algae, and three novel clades ofChloroflexiwere also abundant in the surface soil. During the light hours of the 2007 snow‐free measurement period, CO2uptake was conservatively estimated to be 23.7 g C m−2 season−1. Our study reveals that photoautotrophic microbial communities play an important role in the biogeochemical cycling of subnival zone soil.
Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions
Authors: Martiny Adam C. , Huang Ying , Li Weizhong 
Published: February 2009

SummaryThe cyanobacterium Prochlorococcus is the numerically dominant phototroph in oligotrophic parts of the oceans. Recently, it was shown that the distribution of phosphate acquisition genes did not match the 16S rRNA phylogeny among isolates from this group but rather appeared related to phosphate availability where the strains had been isolated. To further understand adaptation to phosphate limitation in Prochlorococcus, the distribution of phosphate acquisition genes was investigated in different ocean regions and related to local ortho‐phosphate concentration. In regions characterized by less than 0.1 μM phosphate, most Prochlorococcus cells contain genes involved in phosphate uptake, regulation and utilization of organic phosphates. In contrast, most of these genes are absent in regions with more than 0.1 μM phosphate with the exception of genes involved in transport of phosphate (phoE and pstABCS) and three genes of unknown function. This pattern of phosphate acquisition genes showed no significant correspondence to the distribution of rRNA phylotypes. In addition, it was demonstrated that several genes in a separate genomic island were commonly present in low‐P sites while absent in high‐P sites. Overall, this study further demonstrates a linkage between environmental conditions in the ocean and genome content of Prochlorococcus.
Bladder inhibition or excitation by electrical perianal stimulation in a cat model of chronic spinal cord injury
Authors: Wang Jicheng , Liu Hailong , Shen Bing , Roppolo James R. , De Groat William C. , Tai Changfeng 
Published: February 2009

OBJECTIVETo test the hypothesis that perianal electrical stimulation (PES) in chronic spinal cord‐injured (SCI) cats could induce frequency‐dependent inhibitory or excitatory reflex bladder responses.MATERIALS AND METHODSThe experiments were conducted ≥4–5 weeks after spinal cord transection at the T9‐T10 level. PES was applied via a pair of hook electrodes to the perianal skin area in three awake female cats with chronic SCI. A double‐lumen balloon catheter was inserted through the urethra into the bladder to monitor bladder pressure and infuse saline (2–4 mL/min).RESULTSUnder isovolumetric conditions PES at 3–10 Hz significantly inhibited large‐amplitude reflex bladder activity induced by bladder distension above the micturition volume threshold. However, PES at 20–50 Hz induced large‐amplitude bladder contractions when the bladder volume was below the micturition volume threshold. Inhibitory PES (7 Hz) significantly increased the mean (sem) bladder capacity by 40 (10)% when it was applied continuously during cystometrography. The optimum excitatory PES (30 Hz) induced large‐amplitude (>25 cmH2O), long‐duration (>20 s) bladder contractions at a wide range of bladder volumes (10–90% of bladder capacity).CONCLUSIONSThis study showed that activation of pudendal afferent fibres by PES could induce frequency‐dependent reflex bladder responses in awake cats with chronic SCI, indicating that a possible noninvasive treatment based on PES could be developed to restore both continence and micturition function for patients with SCI.