bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Methane Monooxygenase Genes in Mono Lake Suggests That Increased Methane Oxidation Activity May Correlate with a Change in Methanotroph Community Structure
Authors: Lin Ju-Ling , Joye Samantha B. , Scholten Johannes C. M. , Schäfer Hendrik , McDonald Ian R. , Murrell J. Colin 
Published: October 2005

ABSTRACT

Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved
pmoA
sequences showed a broad diversity of aerobic methane oxidizers including the type I methanotrophs
Methylobacter
(the dominant genus),
Methylomicrobium
, and
Methylothermus
, and the type II methanotroph
Methylocystis
. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of
pmoA
using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in methanotroph community composition.
The genus Deficephalobus De Ley & Coomans, 1990 (Cephalobina: Osstellidae) from nature reserves in Costa Rica
Authors: Bongers Tom , Holovachov Oleksandr , Esquivel Alejandro 
Published: October 2005

AbstractTwo species of the genus Deficephalobus, D. mirabilis sp. n. and D. desenderi, are described and illustrated on the basis of material collected in Costa Rica. The new species is characterised by 0.67-1.2 mm long body; bluntly rounded labial region; amphidial aperture one-third of labial region diam. wide; cheilostom barrel-shaped with sclerotised, bar-shaped, cheilorhabdia; gymnostom barrel-shaped with moderately sclerotised lining of gymnostom; stegostom funnel-shaped anteriorly, narrow tubular posteriorly and subdivided into four sets of rhabdia; basal bulb elongate ovoid with weakly developed valvular apparatus; excretory pore opening anterior to nerve ring; ovary tip almost reaching the level of rectum, large spermatheca, postvulval uterine sac shorter than vulval body diameter; female tail elongate conoid and straight, with filiform tail terminus; male tail short conoid with small, ragged, terminal mucro.
Ecanema ecae gen. n., sp. n. (Nematoda: Dorylaimida) from Costa Rica
Authors: Shaheen Azra , Ahmad Wasim 
Published: October 2005

AbstractEcanema gen. n. is described from natural forest in Costa Rica. The new genus is characterised by having distinctly offset lip region, separate lips with distinctly projecting labial papillae, attenuated odontostyle, pharynx rather sac-like, apparently divisible into three regions, large S1N1, distinct cardiac glands, amphidelphic female genital system, short conoid tail and supplements beginning within the range of spicules in males. The type and only species, E. ecae sp. n., is characterised by having 0.87-0.98 mm long body; 19.5-20.5 μm long odontostyle; expanded part of pharynx comprising 36-41% of total neck length; pars refringens vaginae sclerotised and about one anal body diam. long, and conoid tail with acute terminus.
Assessment of inoculation methods in evaluating response of yam cultivars to infection by Scutellonema bradys
Authors: Baimey Hugues , Coyne Danny , Labuschagne Nico 
Published: October 2005

AbstractTwo glasshouse experiments were conducted to assess the influence of three inoculation methods on Scutellonema bradys multiplication on yam (Dioscorea spp.) and on growth and production of the crop. Three separate cultivars of yam were used in the study: two Dioscorea rotundata cultivars (Ala and Kpouna) and one Dioscorea cayenensis (Tabane). One-month-old plants were each inoculated with approximately 1000 S. bradys juveniles and adults. The inoculation methods included inoculation with chopped infected pieces of yam peel (about 0.5 × 0.3 cm2), chopped and blended infected yam peel and a water suspension (200 ml) of extracted nematodes compared with a S. bradys-free yam tuber peel control. The two experiments were harvested at 9 and 4 months after planting. Nematode population densities at harvest were significantly different (P ≤ 0.05) among inoculation methods and among yam cultivars. Higher nematode population densities were recorded on tubers from plants inoculated with unblended peel, followed by those inoculated with blended peel. Inoculation with nematode suspensions yielded the lowest nematode population densities. Inoculation with S. bradys did not affect the vine circumference and the number of tubers. Weights of tubers differed among inoculation methods for two of the three yam cultivars tested (P ≤ 0.05).
Increased penetration of host roots by nematodes after recovery from quiescence induced by root cap exudate
Authors: Hawes Martha , Stock S. Patricia , Flores-Lara Yolanda , Hubbard Jennifer , Schmitt Mark , McClure Michael 
Published: October 2005

AbstractFourteen of 20 plant species surveyed produced root cap exudates that induced a state of reversible quiescence in Meloidogyne incognita and Caenorhabditis elegans. Exudate from six species failed to induce quiescence in either nematode species. Root cap exudates from pea were found to trigger quiescence in populations of plant-parasitic, animal-parasitic, insect-pathogenic, and free-living nematode species. One animal parasite was resistant. Caenorhabditis elegans strains with defects in known metabolic pathways also were screened to explore the potential for using this model system to examine the genetic basis for exudates-induced quiescence (EIQ). All 62 lines tested exhibited wild type sensitivity to root cap exudates and preliminary efforts to obtain viable EIQ-resistant strains by ethyl methanesulphonate (EMS) mutagenesis were unsuccessful. After recovery from EIQ, penetration of alfalfa roots by second-stage juveniles of M. incognita more than doubled within 24 h, compared with controls, and the number of nematodes per root remained high for a week but long-term development and maturation was similar to that of untreated control inoculum. In cucumber, penetration after recovery from EIQ increased by several fold but returned to control levels within 4 days post-inoculation.
Variations in life history parameters and their influence on rate of population increase of different pathogenic isolates of the pine wood nematode, Bursaphelenchus xylophilus
Authors: Wang Yu , Suzuki Kazuo , Sakaue Daisuke , Yamada Toshihiro 
Published: October 2005

AbstractTwo virulent isolates and two avirulent isolates of Bursaphelenchus xylophilus and one isolate of B. mucronatus were used to investigate the relationships between life history parameters, rate of population increase and virulence. The results showed that on fungal cultures of Botrytis cinerea, virulent B. xylophilus completed one generation much faster than did avirulent B. xylophilus and B. mucronatus. There was a tendency that virulent B. xylophilus isolates laid more eggs during the egg laying period than did avirulent populations. Shorter generation time and higher fecundity resulted in a higher rate of population increase. Generation time and fecundity were primary factors determining rate of population increase. Difference in rate of population increase is closely related to variation of virulence: virulent B. xylophilus increased population size at the fastest rate, avirulent B. xylophilus was slower, and B. mucronatus was slowest. It is assumed that similar variations in life history parameters and rate of population increase are also expressed in pine trees and help to explain variation of virulence in the field.
Prey preference and feeding behaviour of the diplogastrid predator Mononchoides gaugleri (Nematoda: Diplogastrida)
Authors: Bilgrami Anwar , Gaugler Randy , Brey Christopher 
Published: October 2005

AbstractPrey preference and feeding behaviour of Mononchoides gaugleri were studied using 11 phytoparasitic nematode species as prey. A full range of prey preferences were detected in no choice and paired choice predator-prey experiments. Meloidogyne incognita, Heterodera mothi and Anguina tritici juveniles (coefficient of preference = 0.92-1.00) were highly preferred as prey by M. gaugleri in all tests. The second tier of prey preference was occupied by the adult Hirschmanniella oryzae, Tylenchorhynchus mashhoodi, Xiphinema americanum and Paratrichodorus christiei (coefficient of preference = 0.19-0.67), and the third tier by Longidorus attenuatus and Helicotylenchus indicus (coefficient of preference = −0.15-−0.57). Hemicriconemoides mangiferae and Hoplolaimus indicus were not preyed upon. Mononchoides gaugleri attacked H. mothi and A. tritici (maximum strike rate (SR)= 92-94%), which has resulted in maximal prey wounding (encounters resulted in wounding (EW) = 46-47%). Longidorus attenuatus was attacked minimally (SR = 42%) with fewest casualties (EW = 21%). Hirschmanniella oryzae, H. mothi and M. incognita were most susceptible (prey susceptibility (PS) = 87.5-93.5%), whereas X. americanum and P. christiei were highly resistant prey species (prey resistance (PR) = 66.7-74.2%). Temperature and prey density governed predator feeding activities, with optimal search duration at 20-30°C and 150-225 prey. The shortest and longest feeding durations of Mononchoides gaugleri were recorded for M. incognita and L. attenuatus, respectively. Predation was density-dependent.
Paratrichodorus divergens sp. n., a new potential virus vector of tobacco rattle virus and additional observations on P. hispanus Roca & Arias, 1986 from Portugal (Nematoda: Trichodoridae)
Authors: de Almeida Santos Maria Susana Newton , Decraemer Wilfrida , de Almeida Maria Teresa Martins , de Oliveira Abrantes Isabel Maria 
Published: October 2005

AbstractDuring a survey of trichodorids in continental Portugal, a new trichodorid species, Paratrichodorus divergens sp. n., was found. It is described and illustrated with specimens from the type locality together with additional morphometric data and photographs of specimens obtained from soil samples collected in seven other localities. The species is characterised in the female by distinct drop-like to triangular oblique vaginal sclerotisations diverging outwards and sperm cells usually distributed all through the uteri, and in the male by thin, almost straight, striated spicules, the two posteriormost precloacal supplements being located relatively close to one another and usually opposite the distal third of the retracted spicules, presence of a slightly bilobed cloacal lip and sperm cells with a sausage-shaped nucleus. Paratrichodorus divergens sp. n. most closely resembles P. hispanus Roca & Arias, 1986 with which it often occurs in mixed populations. Additional information is also provided for P. hispanus. Coding of the features of the new species is given following the identification key of Decraemer and Baujard.
A synopsis of the genus Bursaphelenchus Fuchs, 1937 (Aphelenchida: Parasitaphelenchidae) with keys to species
Authors: Kulinich Oleg , Mota Manuel , Vieira Paulo , Ryss Alexander 
Published: October 2005

AbstractThe 75 valid species of the genus Bursaphelenchus are listed together with their synonyms. Diagnostic characters and their states are discussed and illustrated. Tabular and traditional text keys are provided for the genus. Two new subspecies are proposed to distinguish populations of B. piniperdae and B. poligraphi, as described by Rühm (1956), from the original descriptions of these species published by Fuchs (1937). Known records of Bursaphelenchus species with their associated natural vectors, plants and plant families are given. Dendrograms of species relationships (UPGMA, standard distance: mean character difference) based on combined taxonomic characters and also on spicule characters only, are provided. Discussion as to whether the species groups are natural or artificial (and therefore purely diagnostic) is based on their relationships in the dendrogram and the vector and associated plant ranges of the species. Of the six species groups distinguished, two appear to represent natural assemblages, these being the xylophilus-group (with ten species) and the hunti-group (seven species), of which two, B. cocophilus and B. dongguanensis, form the cocophilus-cluster which is separated on the dendrogram from the main clusters. The remaining four species groups appear to be artificial and purely diagnostic in function, namely the aberrans-group (four species); the eidmanni-group (six species); the borealis-group (five species), and the piniperdae-group (43 species). Two new subspecies, both in the piniperdae-group, viz. B. piniperdae ruehmpiniperdae n. subsp. and B. poligraphi ruehmpoligraphi n. subsp., are proposed and diagnosed from B. piniperdae piniperdae and B. poligraphi poligraphi the respective type subspecies. Bursaphelenchus dongguanensis is regarded as being a valid member of the genus and its transfer to Parasitaphelenchus is rejected.
Rhabditis (Oscheius) colombiana n. sp. (Nematoda: Rhabditidae), a necromenic associate of the subterranean burrower bug Cyrtomenus bergi (Hemiptera: Cydnidae) from the Cauca Valley, Colombia
Authors: Stock S. Patricia , Caicedo Ana , Calatayud Paul 
Published: October 2005

AbstractRhabditis (Oscheius) colombiana n. sp. is described as a necromenic associate of the burrower bug Cyrtomenus bergi (Hemiptera: Cydnidae) collected in the Cauca Valley, Colombia. The new species resembles others of the insectivora-group, viz, Rhabditis (O.) insectivora Körner, 1954 and Rhabditis (O.) lucianii Maupas, 1919, in a number of morphological and life history traits, but can be separated by a combination of morphological and morphometric characters. The most distinctive morphological features that separate R. (O.) colombiana n. sp. from these two Rhabditis species are the total size of both males and females, which are much shorter and slimmer in the new species; the size of the male spicules and the values of ratios b and c. Additionally, molecular data (18S rDNA sequences) and phylogenetic analyses demonstrated the distinctiveness of this species when compared to a number of other Rhabditis (Oscheius) species.
Xiphinema petersmithi Malan, Swart, Meyer & Heyns, 1997, a junior synonym of X. vuittenezi Luc, Lima, Weischer & Flegg, 1964 (Nematoda: Longidoridae)
Authors: Barsi László 
Published: October 2005

AbstractIn the original description of Xiphinema petersmithi, 1997 the species was differentiated from X. vuittenezi, 1964 by its slightly shorter body length and the presence of spines in the uterus. Subsequently, the presence of uterine spines, although not mentioned in the original description, was confirmed in X. vuittenezi. Seven female and two pre-adult paratypes of X. petersmithi were studied and compared with X. vuittenezi. The X. petersmithi paratypes and X. vuittenezi populations studied could not be consistently differentiated by body length. Because of the presence of small spindle-shaped spines in the uteri of both species and the overlapping body length, there is no consistent character to differentiate the two species. Xiphinema petersmithi is therefore proposed as a junior synonym of X. vuittenezi.
Current and future therapeutic approaches in idiopathic pulmonary fibrosis
Authors: Bouros D. , Antoniou K. M. 
Published: October 2005

Idiopathic pulmonary fibrosis (IPF) is a lethal form of idiopathic diffuse lung disorders for which no current treatment is effective. The aim of the present study was to systematically review the current status and novel therapies of IPF, with emphasis on controlled trials.The studies selected included randomised controlled trials using drugs alone and/or in combination for the treatment of adults with IPF and meta-analyses, published in English. Abstracts of identified articles were retrieved and articles possibly fulfilling inclusion criteria were retrieved in full. Two reviewers independently assessed trial quality if there were any included studies. Data quality was based on place of publication and relevance to clinical care.There is a lack of good-quality studies regarding the effectiveness of the most used drugs, including corticosteroids and noncorticosteroid immunosuppressive agents. Oral corticosteroids are the usual treatment. Other therapies either alone or in combination with corticosteroids are widely used, including azathioprine, cyclophosphamide and colchicine. Interestingly, clinical trials with novel drugs, mainly antifibrotic, anticytokine and immunoregulatory, are currently being investigated in various trial phases.In conclusion, at present, there are no evidence-based therapies for idiopathic pulmonary fibrosis. Further controlled studies are warranted to improve the evidence base for clinical practice.
Sequence variation in ligand binding sites in proteins
Authors: Magliery Thomas J , Regan Lynne 
Published: October 2005

Abstract
Background
The recent explosion in the availability of complete genome sequences has led to the cataloging of tens of thousands of new proteins and putative proteins. Many of these proteins can be structurally or functionally categorized from sequence conservation alone. In contrast, little attention has been given to the meaning of poorly-conserved sites in families of proteins, which are typically assumed to be of little structural or functional importance.

Results
Recently, using statistical free energy analysis of tetratricopeptide repeat (TPR) domains, we observed that positions in contact with peptide ligands are more variable than surface positions in general. Here we show that statistical analysis of TPRs, ankyrin repeats, Cys2His2 zinc fingers and PDZ domains accurately identifies specificity-determining positions by their sequence variation. Sequence variation is measured as deviation from a neutral reference state, and we present probabilistic and information theory formalisms that improve upon recently suggested methods such as statistical free energies and sequence entropies.

Conclusion
Sequence variation has been used to identify functionally-important residues in four selected protein families. With TPRs and ankyrin repeats, protein families that bind highly diverse ligands, the effect is so pronounced that sequence "hypervariation" alone can be used to predict ligand binding sites.
Differential range and activity of various forms of the Hedgehog protein
Authors: Dawber Rebecca J , Hebbes Stephen , Herpers Bram , Docquier France , van den Heuvel Marcel 
Published: October 2005

Abstract

Background
The Hedgehog (Hh) family of secreted proteins act as extracellular messengers to control and coordinate growth and differentiation. The mechanism by which Hh protein travels across a field of cells, and results in a range of specific effects relating to the distance from the source, has been the subject of much debate. It has been suggested that the range and activity of the pathway can be linked to modifications of the Hh protein, specifically the addition of lipid groups at N- and C-terminal sites.

Results
Here we have addressed the potency of different forms of Hh protein by expressing these in Drosophila, where we are able to precisely establish pathway activity and range in naïve but responsive tissues. As expected, a construct that can produce all forms of Hh recapitulates endogenous signaling potencies. In comparison, expression of a form that lacks the cholesterol moiety (HhN) leads to an extended range, but the product is less effective at inducing maximal Hh responses. Expression of a point mutant that lacks the N-terminal palmitate binding site shows that the palmitoylation of Hh is absolutely required for activity in this system.

Conclusion
We conclude that the addition of the cholesterol moiety limits the range of the protein and is required for maximal activity, while addition of palmitate is required for all activity. These findings have implications for understanding how Hedgehog proteins move, and thus their potential at influencing distant sites, and concomitantly, how modifications of the signaling protein can affect the efficacy of the response in exposed cells.
Identification of disease causing loci using an array-based genotyping approach on pooled DNA
Authors: Craig David W , Huentelman Matthew J , Hu-Lince Diane , Zismann Victoria L , Kruer Michael C , Lee Anne M , Puffenberger Erik G , Pearson John M , Stephan Dietrich A 
Published: October 2005

Abstract

Background
Pooling genomic DNA samples within clinical classes of disease followed by genotyping on whole-genome SNP microarrays, allows for rapid and inexpensive genome-wide association studies. Key to the success of these studies is the accuracy of the allelic frequency calculations, the ability to identify false-positives arising from assay variability and the ability to better resolve association signals through analysis of neighbouring SNPs.

Results
We report the accuracy of allelic frequency measurements on pooled genomic DNA samples by comparing these measurements to the known allelic frequencies as determined by individual genotyping. We describe modifications to the calculation of k-correction factors from relative allele signal (RAS) values that remove biases and result in more accurate allelic frequency predictions. Our results show that the least accurate SNPs, those most likely to give false-positives in an association study, are identifiable by comparing their frequencies to both those from a known database of individual genotypes and those of the pooled replicates. In a disease with a previously identified genetic mutation, we demonstrate that one can identify the disease locus through the comparison of the predicted allelic frequencies in case and control pools. Furthermore, we demonstrate improved resolution of association signals using the mean of individual test-statistics for consecutive SNPs windowed across the genome. A database of k-correction factors for predicting allelic frequencies for each SNP, derived from several thousand individually genotyped samples, is provided. Lastly, a Perl script for calculating RAS values for the Affymetrix platform is provided.

Conclusion
Our results illustrate that pooling of DNA samples is an effective initial strategy to identify a genetic locus. However, it is important to eliminate inaccurate SNPs prior to analysis by comparing them to a database of individually genotyped samples as well as by comparing them to replicates of the pool. Lastly, detection of association signals can be improved by incorporating data from neighbouring SNPs.
Persistence of lipoatrophy after a four-year long interruption of antiretroviral therapy for HIV1 infection: case report
Authors: Parruti Giustino , Toro Giuseppe Marani 
Published: October 2005

AbstractBackgroundHIV-infected patients on long-term highly active antiretroviral therapy often present peculiar patterns of fat redistribution, referred to as lipodystrophy. In spite of recent investigations, it is not known whether and to what extent the main features of lipodystrophy – that is lipoatrophy of peripheral fat at face, limbs and buttocks, as well as fat accumulation at breasts, abdomen and the dorso-cervical region – can be reversible once clinically manifest.Case presentationA 35 year old Caucasian HIV infected female developed severe diffuse lipodystrophy while on highly active antiretroviral therapy. A remarkable increase of breast size, fat accumulation at waist, and a fat pad on her lumbar spine were paralleled by progressive and disfiguring lipoatrophy of face, limbs and buttocks. The patient decided to interrupt her therapy after 20 months, with a stably suppressed viremia and a CD4 lymphocyte count >500/μL. She could carry on a safe treatment interruption for longer than 4 years. Most sites of fat accumulation switched to nearly normal appearance, whereas lipoatrophy was substantially unchanged at all affected sites.Conclusionour observation provides pictorial evidence that lipoatrophy may not be reversible even under ideal circumstances. Therefore, strategies to prevent lipoatrophy should be considered when defining therapeutic regimens for HIV infected patients, especially those at high risk.