bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of follicular fluids on the growth of porcine preantral follicle and oocyte
Authors: Metoki T. , Iwata H. , Itoh M. , Kasai M. , Takajyo A. , Suzuki A. , Kuwayama T. , Monji Y. 
Published: June 2008

SummaryWe examined the effect of supplementing the culture medium with follicular fluid (FF) on the growth of porcine preantral follicles and oocytes. Firstly, preantral follicles were retrieved from ovaries and then FF was collected from all antral follicles that were 2–7 mm in diameter (AFF), which included large follicles of 4–7 mm in diameter (LFF) and small follicles of 2–3 mm in diameter (SFF). When preantral follicles with a diameter of 250 μm were cultured in medium containing AFF, the growth of follicles and oocytes was greater than when follicles were cultured in medium containing fetal calf serum (FCS). When this growth-promoting effect in AFF was compared for LFF and SFF, the LFF were shown to be significantly more effective than SFF. This LFF effect was lost, however, when the concentration of LFF in the medium was decreased from 5% to 0.5% or when LFF were heat treated (60 °C for 30 min) or trypsin was added. In contrast, a decrease in SFF concentration from 5% to 0.5% and heat treatment of the SFF enhanced preantral follicle growth. Furthermore, proteins obtained from LFF that had molecular weights greater than 10 kDa (LFF > 10 kDa) had similar, but relatively reduced, growth-promoting properties. The remaining three LFF protein fractions (<10 kDa or <100 kDa or >100 kDa), however, did not have these growth-promoting properties. In conclusion, the supplementation of medium with LFF, rather than serum, enhanced preantral follicle and oocyte growth. Factors that enhanced follicle development in LFF and factors that suppressed follicle development in SFF were proteins and these LFF factors ranged in size from 10 kDa to over 100 kDa.
Conserved sequences of sperm-activating peptide and its receptor throughout evolution, despite speciation in the sea star Asterias amurensis and closely related species
Authors: Nakachi Mia , Hoshi Motonori , Matsumoto Midori , Moriyama Hideaki 
Published: June 2008

SummaryThe asteroidal sperm-activating peptides (asterosaps) from the egg jelly bind to their sperm receptor, a membrane-bound guanylate cyclase, on the tail to activate sperm in sea stars. Asterosaps are produced as single peptides and then cleaved into shorter peptides. Sperm activation is followed by the acrosome reaction, which is subfamily specific. In order to investigate the molecular details of the asterosap–receptor interaction, corresponding cDNAs have been cloned, sequenced and analysed from the Asteriinae subfamily including Asterias amurensis, A. rubens, A. forbesi and Aphelasterias japonica, as well as Distolasterias nipon from the Coscinasteriinae subfamily. Averages of 29% and 86% identity were found from the deduced amino acid sequences in asterosap and its receptor extracellular domains, respectively, across all species examined. The phylogenic tree topology for asterosap and its receptor was similar to that of the mitochondrial cytochrome c oxidase subunit I. In spite of a certain homology, the amino acid sequences exhibited speciation. Conservation was found in the asterosap residues involved in disulphide bonding and proteinase-cleaving sites. Conversely, similarities were detected between potential asterosap-binding sites and the structure of the atrial natriuretic peptide receptor. Although the sperm-activating peptide and its receptor share certain common sequences, they may serve as barriers that ensure speciation in the sea star A. amurensis and closely related species.
Secretion of stem cell factor and granulocyte–macrophage colony-stimulating factor by mouse embryos in culture: influence of group culture
Authors: Contramaestre A. P. , Sifontes F. , Marín R. , Camejo M. I. 
Published: June 2008

SummaryPrevious studies showed that the addition of a growth factor to the culture medium could modulate embryo development. The possible secretion of different factors to the culture medium by the embryo itself, however, has been poorly evaluated. The present study was designed to investigate: (1) the influence of single or group culture on the development of 2-cell mouse embryos (strain CD-1) to the blastocyst stage; (2) the release of granulocyte–macrophage colony-stimulating factor (GM-CSF) and stem cell factor (SCF) into the culture medium by the embryo; and (3) the levels of GM-CSF and SCF in the culture medium from both single and group embryos. Two-cell CD-1 mouse embryos were cultured for 96 h singly or in groups of five embryos per drop. GM-CSF and SCF were assayed by ELISA in the complete culture medium. It was found that embryos cultured in groups gave a higher percentage of total blastocyst formation and hatched blastocyst when compared with single embryo culture. The mouse embryos secreted GM-CSF and SCF to the culture medium. The concentration of these cytokines is significantly higher in the group cultures than the level found in single cultures. In conclusion, mouse embryos in culture secrete GM-CSF and SCF to the culture medium and the concentration of these cytokines increases during communal culture. These factors may be operating in both autocrine and paracrine pathways to modulate embryo development during in vitro culture.
Evaluation of chromatin integrity of motile bovine spermatozoa capacitatedin vitro
Authors: Reckova Z. , Machatkova M. , Rybar R. , Horakova J. , Hulinska P. , Machal L. 
Published: June 2008

SummaryThe efficiency ofin vitroembryo production is highly variable amongst individual sires in cattle. To eliminate that this variability is not caused by sperm chromatin damage caused by separation or capacitacion, chromatin integrity was evaluated. Seventeen of AI bulls with good NRRs but variable embryo production efficiency were used. For each bull, motile spermatozoa were separated on a Percoll gradient, resuspended in IVF–TALP medium and capacitated with or incubated without heparin for 6 h. Samples before and after separation and after 3-h and 6-h capacitacion or incubation were evaluated by the Sperm Chromatin Structure Assay (SCSA) and the proportion of sperm with intact chromatin structure was calculated. Based on changes in the non-DFI-sperm proportion, the sires were categorized as DNA-unstable (DNA-us), DNA-stable (DNA-s) and DNA-most stable (DNA-ms) bulls (n= 3,n= 5 andn= 9, respectively). In DNA-us bulls, separation produced a significant increase of the mean non-DFI-sperm proportion (p≤ 0.01), as compared with the value before separation. Capacitacion produced a significant decrease in the mean non-DFI-sperm proportion in H+sperm (p≤ 0.01). In DNA-s bulls, separation significantly increased the mean non-DFI-sperm proportion (p≤ 0.01) but during capacitacion, the mean non-DFI-sperm proportion remained almost unchanged. In DNA-ms bulls, neither separation nor capacitacion had any effect on the mean non-DFI-sperm proportion. It can be concluded that, although separation and capacitacion may produce some changes in sperm chromatin integrity, these are not associated with differentin vitrofertility of the bulls involved.
Seasonal dynamics of the endosymbiotic, nitrogen-fixing cyanobacterium Richelia intracellularis in the eastern Mediterranean Sea
Authors: Zeev Edo Bar , Yogev Tali , Man-Aharonovich Dikla , Kress Nurit , Herut Barak , Béjà Oded , Berman-Frank Ilana 
Published: June 2008

Abstract
Biological nitrogen fixation has been suggested as an important source of nitrogen for the ultra-oligotrophic waters of the Levantine Basin of the Mediterranean Sea. In this study, we identify and characterize the spatial and temporal distribution of the N-fixing (diazotrophic) cyanobacterium Richelia intracellularis. R. intracellularis is usually found as an endosymbiont within diatoms such as Rhizosolenia spp and Hemiaulus spp. and is an important diazotroph in marine tropical oceans. In this study, two stations off the Mediterranean coast of Israel were sampled monthly during 2005–2007. R. intracellularis was identified by microscopy and by reverse transcribed-PCR which confirmed a 98.8% identity with known nifH sequences of R. intracellularis from around the world. The diatom–diazotroph associations were found throughout the year peaking during autumn (October–November) at both stations. Abundance of R. intracellularis ranged from 10 to 55 heterocysts l−1 and correlated positively with the dissolved Si(OH)4/(NO3+NO2) ratio in surface waters. Although the rates of nitrogen fixation were very low, averaging ∼1.1 nmol N l−1 day−1 for the R. intracellularis size fraction (&gt;10 μm) from surface waters, they correlated positively with heterocyst counts during thermal stratification. The lack of large-scale diatom–diazotroph blooms and the low rates of nitrogen fixation by these diazotrophs may result from the P-starved conditions affecting the Levantine basin.
Microbial ecology of the equine hindgut during oligofructose-induced laminitis
Authors: Milinovich Gabriel J , Burrell Paul C , Pollitt Christopher C , Klieve Athol V , Blackall Linda L , Ouwerkerk Diane , Woodland Erika , Trott Darren J 
Published: June 2008

Abstract
Alimentary carbohydrate overload is a significant cause of laminitis in horses and is correlated with drastic shifts in the composition of hindgut microbiota. Equine hindgut streptococcal species (EHSS), predominantly Streptococcus lutetiensis, have been shown to be the most common microorganisms culturable from the equine caecum prior to the onset of laminitis. However, the inherent biases of culture-based methods are estimated to preclude up to 70% of the normal caecal microbiota. The objective of this study was to evaluate bacterial population shifts occurring in the equine caecum throughout the course of oligofructose-induced laminitis using several culture-independent techniques and to correlate these with caecal lactate, volatile fatty acid and degrees of polymerization 3–7 fructo-oligosaccharide concentrations. Our data conclusively show that of the total microbiota present in the equine hindgut, the EHSS S. lutetiensis is the predominant microorganism that proliferates prior to the onset of laminitis, utilizing oligofructose to produce large quantities of lactate. Population shifts in lactobacilli and Escherichia coli subpopulations occur secondarily to the EHSS population shifts, thus confirming that lactobacilli and coliforms have no role in laminitis. A large, curved, Gram-negative rod previously observed during the early phases of laminitis induction was most closely related to the Anaerovibrio genus and most likely represents a new, yet to be cultured, genus and species. Correlation of fluorescence in situ hybridization and quantitative real-time PCR results provide evidence supporting the hypothesis that laminitis is associated with the death en masse and rapid cell lysis of EHSS. If EHSS are lysed, liberated cellular components may initiate laminitis.
Sociobiological Control of Plasmid copy number
Authors: Watve Mukta , Watve Milind 
Published: June 2008

Abstract
Background:
All known mechanisms and genes responsible for the regulation of plasmid replication lie with the plasmid rather than the chromosome. It is possible therefore that there can be copy-up mutants. Copy-up mutants will have within host selective advantage. This would eventually result into instability of bacteria-plasmid association. In spite of this possibility low copy number plasmids appear to exist stably in host populations. We examined this paradox using a computer simulation model.

Model:
Our multilevel selection model assumes a wild type with tightly regulated replication to ensure low copy number. A mutant with slightly relaxed replication regulation can act as a “cheater” or “selfish” plasmid and can enjoy a greater within-host-fitness. However the host of a cheater plasmid has to pay a greater cost. As a result, in host level competition, host cell with low copy number plasmid has a greater fitness. Furthermore, another mutant that has lost the genes required for conjugation was introduced in the model. The non-conjugal mutant was assumed to undergo conjugal transfer in the presence of another conjugal plasmid in the host cell.

Results:
The simulatons showed that if the cost of carrying a plasmid was low, the copy-up mutant could drive the wild type to extinction or very low frequencies. Consequently, another mutant with a higher copy number could invade the first invader. This process could result into an increasing copy number. However above a certain copy number within-host selection was overcompensated by host level selection leading to a rock-paper-scissor (RPS) like situation. The RPS situation allowed the coexistence of high and low copy number plasmids. The non-conjugal “hypercheaters” could further arrest the copy numbers to a substantially lower level.

Conclusions:
These sociobiological interactions might explain the stability of copy numbers better than molecular mechanisms of replication regulation alone.
Ecoinformatics: where are we, where do we want to go, and how to reach there.
Authors: Krishna Abhay 
Published: June 2008

AbstractCompared to other natural sciences ecological sciences has always been about seeing the bigger picture. The realization that local actions can have global impact has been the hallmark of ecological research. This integrative view is getting more and more accepted now with the recognition that whole is definitely more then sum of its parts. Advancement in computer sciences has now made it possible to comprehend the complexity arising from an integrative approach. This has given rise to a field interfacing computer science and ecological sciences called Ecoinformatics. The other popular parallel and more mature field is bioinformatics or computational biology. The presentation will take the audience on an Ecoinformatics tour touching on present status of Ecoinformatics tools and applications, a futuristic account of where Ecoinformatics is heading, and the pragmatic step by step method to transform future into reality; applying insights from lessons learnt from a more mature interface science 'Bioinformatics'. Audience will be introduced to Ecoinformatics projects namely Kepler, Vegbank, Jalama, Knowledge network for biocomplexity (KNB), Science Environment for Ecological Knowledge (SEEK). The presentation will also explore the importance of Ecoinformatics for the icons and upstarts in ecology.
The Management of Encephalitis: Clinical Practice Guidelines by the Infectious Diseases Society of America
Authors: Tunkel Allan R. , Glaser Carol A. , Bloch Karen C. , Sejvar James J. , Marra Christina M. , Roos Karen L. , Hartman Barry J. , Kaplan Sheldon L. , Scheld W. Michael , Whitley Richard J. 
Published: June 2008

Abstract
Guidelines for the diagnosis and treatment of patients with encephalitis were prepared by an Expert Panel of the Infectious Diseases Society of America. The guidelines are intended for use by health care providers who care for patients with encephalitis. The guideline includes data on the epidemiology, clinical features, diagnosis, and treatment of many viral, bacterial, fungal, protozoal, and helminthic etiologies of encephalitis and provides information on when specific etiologic agents should be considered in individual patients with encephalitis.
Is an Increased Dwell Time of a Peripherally Inserted Catheter Associated With an Increased Risk of Bloodstream Infection in Infants?
Authors: Smith P. Brian , Benjamin Daniel K. , Cotten C. Michael , Schultz Eric , Guo Rose , Nowell Lisa , Smithwick Mary Laura , Thornburg Courtney D. 
Published: June 2008

Objective.To estimate the risk of bloodstream infection associated with catheter dwell time in infants.Design.Retrospective study.Setting.Duke University Medical Center neonatal intensive care unit, an academic, level 3 nursery in Durham, North Carolina.Methods.A case of catheter-associated bloodstream infection was defined as one that occurred in an infant whose culture-positive blood sample was collected more than 24 hours after catheter insertion or within 72 hours after catheter removal. We used multivariable logistic regression to control for the catheter's position and dwell time as well as the infant's sex, gestational age, age at time of catheter insertion, birth weight, and weight at time of catheter insertion.Results.We identified 135 cases of catheter-associated bloodstream infection. The mean catheter dwell time was 12.2 days (range, 0–113 days), and the mean time to bloodstream infection was 10.8 days (range, 1–57 days). An increase in catheter dwell time was associated with a lower risk of bloodstream infection (odds ratio, 0.975 [95% confidence interval, 0.954–0.996]; P = .02).Conclusion. Noincreased risk of catheter-associated bloodstream infection was observed with increased catheter dwell time. This may have been due to the infant's improved nutrition, decreased need for other invasive devices, and maturing skin and immune system as catheter dwell time increased.
Comparing simulation results of SBML capable simulators
Authors: Bergmann Frank T. , Sauro Herbert M. 
Published: June 2008

Abstract
Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being able to compare their simulation results.
Summary: We present an approach to compare simulation results between several SBML capable simulators and provide a website for the community to share simulation results.
Availability: The website with simulation results and additional material can be found under: http://sys-bio.org/sbwWiki/compare. The software used to generate the simulation results is available on the website for download.
Contact: fbergman@u.washington.edu
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands
Authors: Srivastava Gyan P. , Guo Juyuan , Shi Huidong , Xu Dong 
Published: June 2008

Abstract
Motivation: DNA methylation plays important roles in biological processes and human diseases, especially cancers. High-throughput bisulfite genomic sequencing based on new generation of sequencers, such as the 454-sequencing system provides an efficient method for analyzing DNA methylation patterns. The successful implementation of this approach depends on the use of primer design software capable of performing genome-wide scan for optimal primers from in silico bisulfite-treated genome sequences. We have developed a method, which fulfills this requirement and conduct primer design for sequences including regions of given promoter CpG islands.
Results: The developed method has been implemented using the C and JAVA programming languages. The primer design results were tested in the PCR experiments of 96 selected human DNA sequences containing CpG islands in the promoter regions. The results indicate that this method is efficient and reliable for designing sequence-specific primers.
Availability: The sequence-specific primer design for DNA meth-ylated sequences including CpG islands has been integrated into the second version of PRIMEGENS as one of the primer design features. The software is freely available for academic use at http://digbio.missouri.edu/primegens/.
Contact: xudong@missouri.edu
Population biology of monkfish Lophius americanus
Authors: Richards R. Anne , Nitschke Paul C. , Sosebee Katherine A. 
Published: June 2008

Abstract
Richards, R. A., Nitschke, P. C., and Sosebee, K. A. 2008. Population biology of monkfish Lophius americanus. – ICES Journal of Marine Science, 65: 1291–1305. This paper provides an overview of the biology of monkfish in US waters of the Northwest Atlantic Ocean using data from resource surveys spanning the period 1948–2007. Monkfish exhibited seasonal onshore–offshore shifts in distribution, migrated out of the southern Mid-Atlantic Bight (MAB) in mid-spring, and re-appeared there in autumn. Sex ratios at length for fish 40–65-cm long were skewed towards males in the southern MAB, but approximated unity elsewhere, suggesting that a portion of the population resides outside sampled areas. Growth was linear at 9.9 cm year−1 and did not differ by region or sex. Maximum observed size was 138 cm for females and 85 cm for males. Length at 50% maturity for males was 35.6 cm (4.1 years old) in the north and 37.9 cm (4.3 years old) in the south; for females 38.8 cm (4.6 years old) in the north and 43.8 cm (4.9 years old) in the south. Ripe females were found in shallow (<50 m) and deep (>200 m) water in the south, and in shallow water (<50 m) in the north.
Expression and Secretion of Cathelicidin LL-37 in Human Epithelial Cells after Infection byMycobacterium bovisBacillus Calmette-Guérin
Authors: Méndez-Samperio Patricia , Miranda Elena , Trejo Artemisa 
Published: June 2008

ABSTRACTThe antimicrobial cathelicidin LL-37 is considered to play an important role in the innate immune response to tuberculosis infection. However, little is known about the induction and secretion of this antimicrobial peptide in A549 epithelial cells after infection withMycobacterium bovisbacillus Calmette-Guérin (BCG), the world's most widely used tuberculosis vaccine. In this study, we investigated the effect ofM. bovisBCG on LL-37 mRNA levels in A549 cells by real-time PCR and on protein levels by Western blotting. Treatment of cells withM. bovisBCG upregulates LL-37 mRNA expression in a dose- and time-dependent manner. The quantitative analysis of LL-37 gene expression correlated with our Western blotting results. Moreover, our results demonstrated that treatment of cells with the transcriptional inhibitor actinomycin D effectively inhibited in a concentration-dependent manner the ability ofM. bovisBCG to induce LL-37 mRNA expression. Finally, inhibition of the MEK1/2 and p38 mitogen-activated protein kinase (MAPK) signaling pathways reducedM. bovisBCG-mediated LL-37 mRNA expression, a reduction that correlated with the observed high level of downregulation of LL-37 protein induction. Thus, these results indicate that the MEK1/2 and p38 MAPK signaling pathways play a critical role in the regulation of inducible LL-37 gene expression in A549 cells infected withM. bovisBCG.