bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behaviour of resampling methods under different weighting schemes, measures and variable resampling strengths
Authors: Kopuchian Cecilia , Ramírez Martín J. 
Published: August 2009

AbstractWe compared general behaviour trends of resampling methods (bootstrap, bootstrap with Poisson distribution, jackknife, and jackknife with symmetric resampling) and different ways to summarize the results for resampling (absolute frequency, F, and frequency difference, GC′) for real data sets under variable resampling strengths in three weighting schemes. We propose an equivalence between bootstrap and jackknife in order to make bootstrap variable across different resampling strengths. Specifically, for each method we evaluated the number of spurious groups (groups not present in the strict consensus of the unaltered data set), of real groups, and of inconsistencies in ranking of groups under variable resampling strengths. We found that GC′ always generated more spurious groups and recovered more groups than F. Bootstrap methods generated more spurious groups than jackknife methods; and jackknife is the method that recovered more real groups. We consistently obtained a higher proportion of spurious groups for GC′ than for F; and for bootstrap than for jackknife. Finally, we evaluated the ranking of groups under variable resampling strengths qualitatively in the trajectories of “support” against resampling strength, and quantitatively with Kendall coefficient values. We found fewer ranking inconsistencies for GC′ than for F, and for bootstrap than for jackknife.© The Willi Hennig Society 2009.
Identification of probiotic lactobacilli used for animal feeds on the basis of 16S ribosomal RNA gene sequence
Authors: Higuchi Wataru , Muramatsu Mineo , Dohmae Soshi , Takano Tomomi , Isobe Hirokazu , Yabe Shizuka , Da Shi , Baranovich Tatiana , Yamamoto Tatsuo 
Published: August 2009

ABSTRACTThe use of probiotics such as Lactobacillus in animal feeds has gained popularity in recent years. In this study the 16S rRNA gene sequence of L. acidophilus in two commercial agents which have been used in animal feeds, LAB‐MOS and Ghenisson 22, was determined. Phylogenetic tree analysis revealed that the two agents, strain MNFLM01 in LAB‐MOS and strain GAL‐2 in Ghenisson 22, belonged to L. rhamnosus (a member of the L. casei group) and L. johnsonii (a member of the L. acidophilus group), respectively. Biochemical tests assigned the two as L. rhamnosus and ambiguously as L. acidophilus. The data suggest that 16S rRNA gene sequence analysis provides more accurate identification of Lactobacillus species than biochemical tests and would allow quality assurance of relevant commercial products. The 16S rRNA gene sequences of strains MNFLM01 and GAL‐2 determined in this study have been submitted to the DDBJ/EMBL/GenBank accession numbers under accession numbers AB288235 and AB295648, respectively.
Analysis of peripheral blood lymphocyte phenotypes and Th1/Th2 cytokines profile in the systemic immune responses of Helicobacter pylori infected individuals
Authors: Kayhan Basak , Arasli Mehmet , Eren Haci , Aydemir Selim , Kayhan Burcak , Aktas Elif , Tekin Ishak 
Published: August 2009

ABSTRACT H. pylori elicits specific humoral and cellular immune responses in the mucosal immune system. However, the type and extent of T lymphocyte response in the systemic immune system is not clear for H. pylori positive patients. In this study, peripheral blood T lymphocyte phenotypes and serum Th1/Th2 based cytokines of 32 H. pylori positive patients were analyzed and compared to those of healthy controls. While αβ TCR+ lymphocytes and their phenotype analysis were not significantly different to those of healthy controls, the percentage of pan γδ TCR+ lymphocytes was up to 2.4 times greater in the H. pylori positive group then in healthy controls. Furthermore, significant increases in IL‐10 concentrations in serum samples of H. pylori patients indicated that their immune systems had switched toward a Th2 type immune response. The correlation between phenotype and type of T cell response in the peripheral blood during H. pylori infection is discussed.
Antimicrobial and anti‐inflammatory activity of five Taxandria fragrans oils in vitro
Authors: Hammer Katherine A. , Carson Christine F. , Dunstan Janet A. , Hale Jasmine , Lehmann Heidi , Robinson Christopher J. , Prescott Susan L. , Riley Thomas V. 
Published: August 2009

ABSTRACTThe antimicrobial activity of five samples of Taxandria fragrans essential oil was evaluated against a range of Gram‐positive (n= 26) and Gram‐negative bacteria (n= 39) and yeasts (n= 10). The majority of organisms were inhibited and/or killed at concentrations ranging from 0.06–4.0% v/v. Geometric means of MIC were lowest for oil Z (0.77% v/v), followed by oils X (0.86%), C (1.12%), A (1.23%) and B (1.24%). Despite differences in susceptibility data between oils, oils A and X did not differ when tested at 2% v/v in a time kill assay against Staphylococcus aureus. Cytotoxicity assays using peripheral blood mononuclear cells demonstrated that T. fragrans oil was cytotoxic at 0.004% v/v but not at 0.002%. Exposure to one or more of the oils at concentrations of ≤0.002% v/v resulted in a dose responsive reduction in the production of proinflammatory cytokines IL‐6 and TNF‐α, regulatory cytokine IL‐10, Th1 cytokine IFN‐γ and Th2 cytokines IL‐5 and IL‐13 by PHA stimulated mononuclear cells. Oil B inhibited the production of all cytokines except IL‐10, oil X inhibited TNF‐α, IL‐6 and IL‐10, oil A inhibited TNF‐α and IL‐6, oil C inhibited IL‐5 and IL‐6 and oil Z inhibited IL‐13 only. IL‐6 production was significantly inhibited by the most oils (A, B, C and X), followed by TNF‐α (oils A, B and X). In conclusion, T. fragrans oil showed both antimicrobial and anti‐inflammatory activity in vitro, however, the clinical relevance of this remains to be determined.
Interaction between cFLIPL and Itch, a ubiquitin ligase, is obstructed in Trypanosoma cruzi‐infected human cells
Authors: Murata Eri , Hashimoto Muneaki , Aoki Takashi 
Published: August 2009

ABSTRACTDeath receptor‐mediated host cell apoptosis, a defense strategy for elimination by the immune system of parasite‐infected cells, is inhibited by Trypanosoma cruzi, the causative agent of Chagas' disease. It has previously been reported by us that, in infected cells, T. cruzi upregulates and exploits cFLIPL, a mammalian inhibitor of death receptor signaling. Here it is shown that ubiquitination of cFLIPL, leading to proteasomal degradation, is inhibited in parasite‐infected cells. The extent of expression of Itch, a protein thought to be an ubiquitin ligase for cFLIPL, was found to be equivalent in T. cruzi‐infected and in uninfected cells. However, co‐immunoprecipitation analysis showed that the interaction between cFLIPL and Itch is strongly inhibited in T. cruzi‐infected cells. This unique parasite strategy, which has not been reported in any other pathogen‐infected cells, may allow the host cell to accumulate cFLIPL, eventually resulting in the inhibition of apoptosis of T. cruzi‐infected cells.
Some aspects of the biology of the stargazer mountain catfish, Amphilius uranoscopus (pfeffer); (Siluriformes: Amphiliidae) indigenous to Kenya streams
Authors: Ngugi Charles C. , Manyala Julius O. , Njiru Murithi , Mlewa Chrisestom M. 
Published: August 2009

AbstractA study on some biological parameters of the mountain catfish, Amphilius uranoscopus Pfeffer 1889 (Silurifomes: Amphiliidae), was carried out in the Thego stream on the slopes of Mount Kenya from February to December 2002. Physical and chemical profiles of the Thego show that the water quality parameters is typical of high altitude streams with temperatures rarely exceeding 18°C, DO ranging from 7.9 to 8.2 mg l−1 and relatively high conductivity (97–137 μS cm−1) typical of perturbed lotic environments. A total of 1010 fish were caught by an electro‐fisher, with sizes ranging between 8 and 24 cm fork length. The population structure had a unimodal distribution with maxima at 14–16 cm. The length–weight relationship showed relatively narrow range in the slope ranging from 2.61 in April to 2.98 in February 2002, thereby suggesting isometric growth pattern. The fitted growth pattern of A. uranoscopus showed an asymptotic length (L∞) of 28.5 cm and a growth curvature (K) of 0.56 year−1 resulting in an estimated natural mortality coefficient (M) of 0.90 year−1. The Fulton’s condition factor (K) was also relatively stable with a peak in April (0.92 ± 0.21) and lowest value in June (0.86 ± 0.10). As A. uranoscopus is not under commercial exploitation, the seemingly depressed population is possibly attributed to the introduced exotic rainbow trout that heavily predates on the species and environmental perturbations arising from changes in land use. The implications of such changes on A. uranoscopus are discussed.
Whole‐genome scan for guttural pouch tympany in Arabian and German warmblood horses
Authors: Zeitz A. , Spötter A. , Blazyczek I. , Diesterbeck U. , Ohnesorge B. , Deegen E. , Distl O. 
Published: August 2009

SummaryEquine guttural pouch tympany (GPT) is a hereditary disease in foals of several breeds, including thoroughbreds, Arabian, Quarter and warmblood horses. We performed a whole‐genome scan for GPT in 143 horses from five Arabian and five German warmblood families and genotyped 257 microsatellites. Chromosome‐wide significant linkage was detected on ECA2 and ECA15 using multipoint non‐parametric linkage analyses. Analyses stratified by sex revealed chromosome‐wide significant linkage on ECA2 for fillies and chromosome‐wide significant linkage on ECA15 for colts. For Arabian colts, the quantitative trait locus (QTL) on ECA15 was genome‐wide significant. Haplotypes including two to four microsatellites within the QTL on ECA2 and 15 in fillies and colts, respectively, were significantly associated with GPT for both breeds. Thus, our analysis indicated sex‐specific QTL, a fact which is in agreement with a two‐ to fourfold higher incidence of GPT in females. This is the first report of QTL for equine GPT and a first step towards identifying genes responsible for GPT.
Pteropus vampyrus, a hunted migratory species with a multinational home‐range and a need for regional management
Authors: Epstein Jonathan H. , Olival Kevin J. , Pulliam Juliet R.C. , Smith Craig , Westrum Justin , Hughes Tom , Dobson Andrew P. , Zubaid Akbar , Rahman Sohayati Abdul , Basir Misliah Mohamad , Field Hume E. , Daszak Peter 
Published: August 2009

Summary 1. The management of migratory species is challenging because of insufficient data on long‐range movement patterns, habitat use, and the impact of anthropogenic pressures (e.g. hunting) throughout their home ranges. 2. We evaluate the current abundance and mobility of the Malayan flying fox Pteropus vampyrus, a threatened fruit bat species of ecological and economic significance across Southeast Asia, using roost site surveys and satellite telemetry. We combined this with data from hunter license sales and population projection models to assess the impact and sustainability of current hunting practices in Peninsular Malaysia. 3. We monitored 33 active Pteropus vampyrus roost sites in Peninsular Malaysia, including eight seasonal roost sites. Roost site occupancy showed considerable temporal variation over the 3‐year study period. 4. Hunting activity has more than doubled since 1996, and based on license sales, we estimate that a minimum legal harvest of 87 800 bats occurred between 2002 and 2005. Population models suggest that this level of hunting is likely to be unsustainable given our baseline abundance scenarios of 100 000, 250 000 or 500 000 bats, especially considering that these models do not include culling of Malayan flying foxes as agricultural pests or illegal hunting activities, for which there are no available data. 5. Satellite telemetry of seven adult male bats show that Malayan flying foxes are highly mobile, travelling hundreds of kilometres between roosting sites within a year and occupying home ranges that extend beyond Malaysia to include Indonesia and Thailand. We conclude that focal hunting pressure in Malaysia threatens a regional population of this migratory mammal. 6.
Synthesis and applications. This is the first study of its kind on flying foxes in Asia, and illustrates that bats, like other migratory species, urgently require comprehensive protection by regional management plans across their range. P. vampyrus moves across international borders in Southeast Asia. Current hunting practices within Malaysia together with limited protection in other countries may threaten its long‐term survival.
Crop damage increases with pest species diversity: evidence from potato tuber moths in the tropical Andes
Authors: Dangles Olivier , Mesías Verónica , Crespo‐Perez Verónica , Silvain Jean‐François 
Published: August 2009

Summary1. Insect pests in agricultural systems are one of the major causes of damage to crop production and storage worldwide. However, the study of the effect of multiple pests on agricultural productivity has remained largely disconnected from the ongoing debate on how species diversity affects the productivity of ecosystems. The aim of our study is to use information from crop studies to inform the debate on species diversity and ecosystem productivity.2. We present the results of an experimental study that manipulated the species richness of three tuber feeding moth species (Lepidoptera: Gelechiidae) at constant larval density. We measured the influence of this manipulation on (1) damage to the economically most important crop in the Andean region, the potatoSolanum tuberosumand (2) the performance of the moths as a consequence of feeding rates.3. Our results showed that the three pest species together cause more damage to the crop than is predicted from the effects of each pest alone. This resulted in significant increases in pupal biomass and fecundity.4. Potential mechanisms to explain our results are (1) more complete resource utilization and thus greater crop damage (feeding complementarity) and (2) negative interactions, where intra‐specific interactions are greater than inter‐specific interactions.5.Synthesis and applications. Our findings may have important consequences for integrated pest management in poor tropical countries. Biodiversity in many tropical countries is decreasing rapidly, leading to reductions in ecosystem services such as biocontrol and pollination. At the same time an increasing number of species, many of them agricultural pests, are being introduced by humans. Our results show that the potential complementarity effects among pest species may increase damage to field crops to a larger extent than previously expected. Control strategies to limit the introduction of new pest species are therefore urgently needed in these countries where the daily management of biological resources is largely in the hands of poor rural people and local government staff with limited funding.
Fossil evidence and phylogeography of temperate species: ‘glacial refugia’ and post‐glacial recolonization
Authors: Sommer Robert S. , Zachos Frank E. 
Published: August 2009

AbstractWe present a short synthesis of the Pleistocene distribution dynamics and phylogeographic recolonization hypotheses for two temperate European mammal species, the red deer (Cervus elaphus) and the roe deer (Capreolus capreolus), for which high‐resolution patterns of fossil evidence and genetic data sets are available. Such data are critical to an understanding of the role of hypothesized glacial refugia. Both species show a similar pattern: a relatively wide distribution in the southern part of Central Europe 60,000–25,000 years ago, and a strong restriction to areas in southern Europe for nearly 10,000 years during the Last Glacial Maximum (LGM) and the early Late Glacial (25,000–14,700 years ago). With the beginning of Greenland Interstadial 1 (Bølling/Allerød warming, c. 14,700–11,600 years ago) a sudden range expansion into Central Europe is visible, but the colonization of most of Central Europe, including the northern European Lowlands, only began in the early Holocene. In a European context, regions where the species were distributed during the LGM and early Late Glacial are most relevant as potential origins of recolonization processes, because during these c. 10,000 years distribution ranges were smaller than at any other time in the Late Quaternary. As far as the present distribution of temperate species and their genetic lineages is concerned, so‐called ‘cryptic refugia’ are important only if the species are actually confirmed there during the LGM, as otherwise they could not possibly have contributed to the recolonization that eventually resulted in the present distribution ranges.
Non‐canonical RNA arrangement in T4‐even phages: accommodated ribosome binding site at the gene 26‐25 intercistronic junction
Authors: Malys Naglis , Nivinskas Rimas 
Published: August 2009

SummaryTranslational initiation region of bacteriophage T4 gene 25 contains three potential Shine and Dalgarno sequences: SD1, SD2 and SD3. Mutational analysis has predicted that an mRNA stem‐loop structure may include SD1 and SD2, bringing the most typical sequence SD3, GAGG, to the initiation codon. Here, we report physical evidence demonstrating that previously predicted mRNA stem‐loop structure indeed exists in vivo during gene 25 expression in T4‐infected Escherichia coli cells. The second mRNA stem‐loop structure is identified 14 nucleotides upstream of the stem‐loop I, while the SD3 sequence, as well as the start codon of the gene, are proved to be within an unfolded stretch of mRNA. Phylogenetic comparison of 38 T4‐like phages reveals that the T‐even and some pseudoT‐even phages evolve a similar structural strategy for the translation initiation of 25, while pseudoT‐even, schizoT‐even and exoT‐even phages use an alternative mRNA arrangement. Taken together, the results indicate that a specific mRNA fold forms the split ribosome binding site at the gene 26‐25 intercistronic junction, which is highly competent in the translational initiation. We conclude that this ribosome binding site has evolved after T‐even diverged from other T4‐like phages. Additionally, we determine that the SD sequence GAGG is most widespread in T4.
Clonally variant gene families in Plasmodium falciparum share a common activation factor
Authors: Howitt Cali A. , Wilinski Daniel , Llinás Manuel , Templeton Thomas J. , Dzikowski Ron , Deitsch Kirk W. 
Published: August 2009

SummaryThe genome of the malaria parasite Plasmodium falciparum contains several multicopy gene families, including var, rifin, stevor and Pfmc‐2TM. These gene families undergo expression switching and appear to play a role in antigenic variation. It has recently been shown that forcing parasites to express high copy numbers of transcriptionally active, episomal var promoters led to gradual downregulation and eventual silencing of the entire var gene family, suggesting that a limiting titratable factor plays a role in var gene activation. Through similar experiments using rifin, stevor or Pfmc‐2TM episomal promoters we show that promoter titration can be used as a general method to downregulate multicopy gene families in P. falciparum. Additionally, we show that promoter titration with var, rifin, stevor or Pfmc‐2TM episomal promoters results in downregulation of expression not only of the family to which the episomal promoter belongs, but also members of the other gene families, suggesting that the var‐specific titratable factor previously described is shared by all four families. Further, transcriptionally active promoters from different families colocalize within the same subnuclear expression site, indicating that the role that nuclear architecture plays in var gene regulation also likely applies to the other multicopy gene families of P. falciparum.
Symmetric signalling within asymmetric dimers of the Staphylococcus aureus receptor histidine kinase AgrC
Authors: George Cisar Elizabeth A. , Geisinger Edward , Muir Tom W. , Novick Richard P. 
Published: August 2009

SummaryVirulence in Staphylococcus aureus is largely under control of the accessory gene regulator (agr) quorum‐sensing system. The AgrC receptor histidine kinase detects its autoinducing peptide (AIP) ligand and generates an intracellular signal resulting in secretion of virulence factors. Although agr is a well‐studied quorum‐sensing system, little is known about the mechanism of AgrC activation. By co‐immunoprecipitation analysis and intermolecular complementation of receptor mutants, we showed that AgrC forms ligand‐independent dimers that undergo trans‐autophosphorylation upon interaction with AIP. Remarkably, addition of specific AIPs to AgrC mutant dimers with only one functional sensor domain caused symmetric activation of either kinase domain despite the sensor asymmetry. Furthermore, mutant dimers involving one constitutive protomer demonstrated ligand‐independent activity, irrespective of which protomer was kinase deficient. These results demonstrate that signalling through either individual AgrC protomer causes symmetric activation of both kinase domains. We suggest that such signalling across the dimer interface may be an important mechanism for dimeric quorum‐sensing receptors to rapidly elicit a response upon signal detection.
An outer membrane protease of the omptin family prevents activation of the Citrobacter rodentium PhoPQ two‐component system by antimicrobial peptides
Authors: Le Sage Valerie , Zhu Lei , Lepage Christine , Portt Andrea , Viau Charles , Daigle France , Gruenheid Samantha , Le Moual Hervé 
Published: August 2009

SummaryThe PhoPQ two‐component system of the intracellular pathogen Salmonella enterica senses and controls resistance to α‐helical antimicrobial peptides (AMPs) by regulating covalent modifications of lipid A. A homologue of the phoPQ operon was found in the genome of the murine enteric extracellular pathogen, Citrobacter rodentium. Here we report that C. rodentium PhoPQ was apparently unable to mediate activation of target genes in the presence of α‐helical AMPs. However, these AMPs activated C. rodentium PhoPQ expressed in a S. entericaΔphoPQ mutant. Analysis of the outer membrane (OM) fractions of the C. rodentium wild‐type and ΔphoPQ strains led to the identification of an omptin family protease (CroP) that was absent in ΔphoPQ. Deletion of croP in C. rodentium resulted in higher susceptibility to α‐helical AMPs, indicating a direct role of CroP in AMP resistance. CroP greatly contributed to the protection of the OM from AMP damage by actively degrading α‐helical AMPs before they reach the periplasmic space. Accordingly, transcriptional activation of PhoP‐regulated genes by α‐helical AMPs was restored in the ΔcroP mutant. This study shows that resistance to α‐helical AMPs by the extracellular pathogen C. rodentium relies primarily on the CroP OM protease.