bluuebunny/crossref_metadata_2025 huggingface dataset:
A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
Authors: Nagy Istvan , Barth Susanne , Mehenni-Ciz Jeanne , Abberton Michael T , Milbourne Dan
Published: February 2013

Background

White clover (Trifolium repensL.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. We illustrate one potential approach in this study.

Results

We used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase.

Conclusions

In total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. This represents a significant resource for white clover genomics and genetics studies. We discuss the potential to extend the analysis to identify a “core set” of ancestrally derived homeolog specific variants in white clover.
AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications
Authors: Van Geystelen Anneleen , Decorte Ronny , Larmuseau Maarten HD
Published: February 2013

Background

Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.

Results

We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.

Conclusions

Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.
S-Adenosyl-L-Methionine protects the probiotic yeast, Saccharomyces boulardii,from acid-induced cell death
Authors: Cascio Vincent , Gittings Daniel , Merloni Kristen , Hurton Matthew , Laprade David , Austriaco Nicanor
Published: February 2013

Background

Saccharomyces boulardii is a probiotic yeast routinely used to prevent and to treat gastrointestinal disorders, including the antibiotic-associated diarrhea caused by Clostridium difficile infections. However, only 1-3% of the yeast administered orally is recovered alive in the feces suggesting that this yeast is unable to survive the acidic environment of the gastrointestinal tract.

Results

We provide evidence that suggests that S. boulardii undergoes programmed cell death (PCD) in acidic environments, which is accompanied by the generation of reactive oxygen species and the appearance of caspase-like activity. To better understand the mechanism of cell death at the molecular level, we generated microarray gene expression profiles of S. boulardii cells cultured in an acidic environment. Significantly, functional annotation revealed that the up-regulated genes were significantly over-represented in cell death pathways Finally, we show that S-adenosyl-L-methionine (AdoMet), a commercially available, FDA-approved dietary supplement, enhances the viability of S. boulardii in acidic environments, most likely by preventing programmed cell death.

Conclusions

In toto, given the observation that many of the proven health benefits of S. boulardii are dependent on cell viability, our data suggests that taking S. boulardii and AdoMet together may be a more effective treatment for gastrointestinal disorders than taking the probiotic yeast alone.
Clustering subspecies of Aeromonas salmonicida using IS630typing
Authors: Studer Nicole , Frey Joachim , Vanden Bergh Philippe
Published: February 2013

Background

The insertion element IS630 found in Aeromonas salmonicida belongs to the IS630-Tc1-mariner superfamily of transposons. It is present in multiple copies and represents approximately half of the IS present in the genome of A. salmonicida subsp. salmonicida A449.

Results

By using High Copy Number IS630 Restriction Fragment Length Polymorphism (HCN-IS630-RFLP), strains of various subspecies of Aeromonas salmonicida showed conserved or clustering patterns, thus allowing their differentiation from each other. Fingerprints of A. salmonicida subsp. salmonicida showed the highest homogeneity while ‘atypical’ A. salmonicida strains were more heterogeneous. IS630 typing also differentiated A. salmonicida from other Aeromonas species. The copy number of IS630 in Aeromonas salmonicida ranges from 8 to 35 and is much lower in other Aeromonas species.

Conclusions

HCN-IS630-RFLP is a powerful tool for subtyping of A. salmonicida. The high stability of IS630 insertions in A. salmonicida subsp. salmonicida indicates that it might have played a role in pathoadaptation of A. salmonicida which has reached an optimal configuration in the highly virulent and specific fish pathogen A. salmonicida subsp. salmonicida.
Adipose stromal cells primed with hypoxia and inflammation enhance cardiomyocyte proliferation rate in vitro through STAT3 and Erk1/2
Authors: Przybyt Ewa , Krenning Guido , Brinker Marja GL , Harmsen Martin C
Published: February 2013

Background

Experimental clinical stem cell therapy has been used for more than a decade to alleviate the adverse aftermath of acute myocardial infarction (aMI). The post-infarcted myocardial microenvironment is characterized by cardiomyocyte death, caused by ischemia and inflammation. These conditions may negatively affect administered stem cells. As postnatal cardiomyocytes have a poor proliferation rate, while induction of proliferation seems even more rare. Thus stimulation of their proliferation rate is essential after aMI. In metaplastic disease, the pro-inflammatory cytokine interleukin-6 (IL-6) has been identified as potent mediators of the proliferation rate. We hypothesized that IL-6 could augment the proliferation rate of (slow-)dividing cardiomyocytes.

Methods

To mimic the behavior of therapeutic cells in the post-infarct cardiac microenvironment, human Adipose Derived Stromal Cells (ADSC) were cultured under hypoxic (2% O2) and pro-inflammatory conditions (IL-1β) for 24h. Serum-free conditioned medium from ADSC primed with hypoxia and/or IL-1β was added to rat neonatal cardiomyocytes and adult cardiomyocytes (HL-1) to assess paracrine-driven changes in cardiomyocyte proliferation rate and induction of myogenic signaling pathways.

Results

We demonstrate that ADSC enhance the proliferation rate of rat neonatal cardiomyocytes and adult HL-1 cardiomyocytes in a paracrine fashion. ADSC under hypoxia and inflammation in vitro had increased the interleukin-6 (IL-6) gene and protein expression. Similar to conditioned medium of ADSC, treatment of rat neonatal cardiomyocytes and HL-1 with recombinant IL-6 alone also stimulated their proliferation rate. This was corroborated by a strong decrease of cardiomyocyte proliferation after addition of IL-6 neutralizing antibody to conditioned medium of ADSC. The stimulatory effect of ADSC conditioned media or IL-6 was accomplished through activation of both Janus Kinase-Signal Transducer and Activator of Transcription (JAK/STAT) and Mitogen-Activated Protein (MAP) kinases (MAPK) mitogenic signaling pathways.

Conclusion

ADSC are promising therapeutic cells for cardiac stem cell therapy. The inflammatory and hypoxic host post-MI microenvironment enhances the regenerative potential of ADSC to promote the proliferation rate of cardiomyocytes. This was achieved in paracrine manner, which warrants the development of ADSC conditioned medium as an “of-the-shelf” product for treatment of post-myocardial infarction complications.
An integrated experimental and modeling approach to propose biotinylated PLGA microparticles as versatile targeting vehicles for drug delivery
Authors: Donaldson Olivia , Huang Zuyi Jacky , Comolli Noelle
Published: February 2013

Polymeric microparticles with covalently attached biotin are proposed as versatile targeting vehicles for drug delivery. The proposed microparticles made of 85/15 poly (lactic-co-glycolic acid) (PLGA) will have biotin available on the outside of the particle for the further attachment with an avidin group. Taking advantage of biotin’s high affinity for avidin, and avidin’s well-known chemistry, the particle has the potential to be easily coated with a variety of targeting moieties. This paper focuses on the design and resulting effect of adding biotin to PLGA microparticles using an integrated experimental and modeling approach. A fluorescent-tagged avidin (488-streptavidin) was used to confirm the presence and bioavailability of biotin on the outside of the particles. For the purpose of this study, bovine serum albumin (BSA) was used as a model therapeutic drug. Microparticles were created using two different types of polyvinyl alcohol 88 and 98 mol% hydrolyzed, which were then analyzed for their size, morphology, and encapsulation capacity of BSA. Release studies performed in vitro confirmed the slow release of the BSA over a 28-day period. Based on these release profiles, a release kinetics model was used to further quantify the effect of biotinylation of PLGA microparticles on their release characteristics by quantitatively extracting the effective drug diffusivity and drug desorption rate from the release profiles. It was found that the biotinylation of the PLGA microparticles slowed down both the drug desorption and drug diffusion process, which confirmed that biotinylated PLGA microparticles can be used for controlled drug release. The presented technology, as well as the proposed integrated experimental and modeling approach, forms a solid foundation for future studies using a cell-specific ligand that can be attached to avidin and incorporated onto the microparticles for targeted delivery.
Analysis of myeloperoxidase activity in wound fluids as a marker of infection
Authors: Hasmann A , Wehrschuetz-Sigl E , Marold A , Wiesbauer H , Schoeftner R , Gewessler U , Kandelbauer A , Schiffer D , Schneider K P , Binder B , Schintler M , Guebitz G M
Published: February 2013

Background

Neutrophilic polymorphonuclear leukocytes play a crucial role in the host defence against bacterial and fungal infections. They participate in the inflammatory response through the liberation of peptides and enzymes like myeloperoxidase (MPO). Therefore, MPO has a potential as a marker enzyme for the diagnosis of wound infection.

Methods

Substrate specificities and reaction pathways of MPO were investigated for new MPO substrates: crystal violet, leuco crystal violet, fast blue RR (4-benzoylamino-2,5-dimethoxybenzenediazonium chloride hemi(zinc chloride) salt) and various systematically substituted model substrates based on 2,7-dihydroxy-1-(4-hydroxyphenylazo)naphtalene-3,6-disulphonic acid. In addition, fast blue RR was covalently bound to siloxanes allowing immobilization of the substrate, while cellobiosedehydrogenase was integrated for generation of hydrogen peroxide required by MPO.

Results

Elevated concentrations of MPO were found in infected wounds compared with non-infected wounds (92.2 ± 45.0 versus 1.9 ± 1.8 U/mL). Various soluble and immobilized substrates were oxidized by MPO in wound samples and the influence of substrate structure and reaction pathways were elucidated for selected compounds.

Conclusions

Incubation of different MPO substrates with infected wound fluid samples resulted in a clear colour change in the case of elevated MPO concentrations, thus allowing early diagnosis of wound infection.
Adult testosterone and calculated free testosterone reference ranges by tandem mass spectrometry
Authors: Neale S M , Hocking R , Biswas M , Turkes A , Rees D , Rees D A , Evans C
Published: February 2013

Background

Testosterone is measured for the investigation of female hyperandrogenism and male hypogonadism. Liquid chromatographytandem mass spectrometry (tandem MS) is becoming the method of choice but comprehensive reference ranges are lacking.

Methods

Testosterone was measured by tandem MS on 90 healthy women, 67 young healthy men and pregnant women (59 first trimester and 60 second trimester).

Results

The male, male calculated free, first trimester and second trimester testosterone reference ranges (derived using the antilog of mean ± 1.96 SD of log transformed data) were 10.6-31.9, 0.23-0.63, 0.6-4.9 and 0.9-4.9 nmol/L, respectively. The female testosterone upper reference range limit, derived non-parametrically from the 97.5th centile, was < 1.7 nmol/L.

Conclusions

We have derived tandem MS testosterone reference ranges to support clinical services.
Persistence of Integration in the Face of Specialization: How Firms Navigated the Winds of Disintegration and Shaped the Architecture of the Semiconductor Industry
Authors: Kapoor Rahul
Published: February 2013

Although the stylized model of industry evolution suggests that firms transform from vertical integration to specialization over time, many industries still exhibit a continued persistence of integrated firms. In exploring this puzzle, I draw on detailed firm-level data from the semiconductor industry to analyze how integrated incumbents, beyond shifting to the specialized mode, reconfigured in the face of industry’s vertical disintegration so as to coexist with the specialized firms. I propose and find that the incumbents who persist with vertical integration increase their emphasis on systemic innovations and transact with specialized firms in both upstream and intermediate markets. The value-creating opportunities associated with integrated incumbents’ leveraging (a) their relative superiority in developing systemic innovations and (b) markets to pursue a broader menu of transactional choices may offset their costs of staying integrated. These firm-level factors also determine the pattern of industry’s vertical disintegration and the extent of coexistence between integrated and specialized firms.
Using Civil Processes in Pursuit of Criminal Law Objectives: A Case Study of Non-Conviction-Based Asset Forfeiture
Authors: King Colin
Published: February 2013

Conventional understanding distinguishes between criminal law (and procedures) and civil law (and procedures). These distinctions often rest upon differences as to the moving party, the culpability of a wrongdoer, the nature of a wrong, the remedy available, etc. to determine whether a particular action ought to fall upon the civil or the criminal side of the paradigmatic divide. These distinctions, however, prove problematic in relation to hybrid systems of justice, given legislative attempts to pursue criminal law objectives using civil processes. Using the non-conviction-based asset forfeiture model adopted in Ireland, and drawing upon the test adopted by the US Supreme Court as to what distinguishes the civil from the criminal, this article examines how the Irish judiciary has responded to this approach, ultimately contending that the courts have failed to provide a check against the legislature circumventing enhanced procedural protections of the criminal process and imposing punishment in the civil forum. The article concludes by asking whether a hybrid, or middle-ground, process, in which some enhanced procedural protections are afforded to a person confronted with punitive civil sanctions, offers an alternative to the rigid confines of the conventional civil/criminal dichotomy.
The Case in Australia for Further Reform to the Cross-Examination and Court Management of Child Witnesses
Authors: Caruso David , Cross Timothy
Published: February 2013

Recent legislative reforms in Australia designed to address the difficulties attending the reception and treatment of child evidence will have little, if any, success because they do not address the reasons for the difficulties, nor introduce improvements to existing practice for the child witness, counsel or court.
The Standard of Proof in Civil Cases: An Insurance Fraud Perspective
Authors: Hjalmarsson Johanna
Published: February 2013

This article discusses the burden and standard of proof as they apply to cases of insurance fraud, and notes some important historical developments in the law. The tremendous importance of the exact burden and standard of proof arises from the fact that fraud by its very nature is something that the perpetrator will wish to conceal and that there will be very little proof of any nature available or accessible. The insurer may easily find itself bringing complicated circumstantial evidence as to such elusive matters as the insured's general financial situation; the reasonableness of the valuation of the ship; or the communications that took place between the insured and third parties, perhaps requiring extensive procedural disclosure.
RETRACTED: Stabilization of LCD devices via geometric alteration
Authors: Jeon Il , Yoon MinSung , Lee Je-Hoon
Published: February 2013

"Stabilization of LCD devices via geometric alteration" has been retracted at the request of the authors.
Comparative evaluation of the My5-FU™ immunoassay and LC-MS/MS in monitoring the 5-fluorouracil plasma levels in cancer patients
Authors: Büchel Barbara , Sistonen Johanna , Joerger Markus , Aebi Yolanda , Schürch Stefan , Largiadèr Carlo R.
Published: February 2013

Background: Chemotherapies of solid tumors commonly include 5-fluorouracil (5-FU). With standard doses of 5-FU, substantial inter-patient variability has been observed in exposure levels and treatment response. Recently, improved outcomes in colorectal cancer patients due to pharmacokinetically guided 5-FU dosing were reported. We aimed at establishing a rapid and sensitive method for monitoring 5-FU plasma levels in cancer patients in our routine clinical practice.

Methods: Performance of the Saladax My5-FU™ immunoassay was evaluated on the Roche Cobas® Integra 800 analyzer. Subsequently, 5-FU concentrations of 247 clinical plasma samples obtained with this assay were compared to the results obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and other commonly used clinical analyzers (Olympus AU400, Roche Cobas c6000, and Thermo Fisher CDx90).

Results: The My-FU assay was successfully validated on the Cobas Integra 800 analyzer in terms of linearity, precision, accuracy, recovery, interference, sample carryover, and dilution integrity. Method comparison between the Cobas Integra 800 and LC-MS/MS revealed a proportional bias of 7% towards higher values measured with the My5-FU assay. However, when the Cobas Integra 800 was compared to three other clinical analyzers in addition to LC-MS/MS including 50 samples representing the typical clinical range of 5-FU plasma concentrations, only a small proportional bias (≤1.6%) and a constant bias below the limit of detection was observed.

Conclusions: The My5-FU assay demonstrated robust and highly comparable performance on different analyzers. Therefore, the assay is suitable for monitoring 5-FU plasma levels in routine clinical practice and may contribute to improved efficacy and safety of commonly used 5-FU-based chemotherapies.
Indirect determination of pediatric blood count reference intervals
Authors: Zierk Jakob , Arzideh Farhad , Haeckel Rainer , Rascher Wolfgang , Rauh Manfred , Metzler Markus
Published: February 2013

Background: Determination of pediatric reference intervals (RIs) for laboratory quantities, including hematological quantities, is complex. The measured quantities vary by age, and obtaining samples from healthy children is difficult. Many widely used RIs are derived from small sample numbers and are split into arbitrary discrete age intervals. Use of intra-laboratory RIs specific to the examined population and analytical device used is not yet fully established. Indirect methods address these issues by deriving RIs from clinical laboratory databases which contain large datasets of both healthy and pathological samples.

Methods: A refined indirect approach was used to create continuous age-dependent RIs for blood count quantities and sodium from birth to adulthood. The dataset for each quantity consisted of 60,000 individual samples from our clinical laboratory. Patient samples were separated according to age, and a density function of the proportion of healthy samples was estimated for each age group. The resulting RIs were merged to obtain continuous RIs from birth to adulthood.

Results: The obtained RIs were compared to RIs generated by identical laboratory instruments, and to population-specific RIs created using conventional methods. This comparison showed a high concordance of reference limits and their age-dependent dynamics.

Conclusions: The indirect approach reported here is well-suited to create continuous, intra-laboratory RIs from clinical laboratory databases and showed that the RIs generated are comparable to those created using established methods. The procedure can be transferred to other laboratory quantities and can be used as an alternative method for RI determination where conventional approaches are limited.
BRAF gene polymorphism (rs10487888) assessment in chronic periodontitis and peri-implantitis in an Iranian population
Authors: Kadkhodazadeh Mahdi , Jafari Ali Reza , Khalighi Hamid Reza , Ebadian Ahmad Reza , Vaziri Shahram , Amid Reza
Published: February 2013

Background: Peri-implantitis (PI) and chronic periodontitis (CP) are multifactorial diseases of implant/tooth supporting tissue that are caused by bacterial infection and increased host immune response. T-cell proliferation plays a pivotal role in the orchestration of host response to bacterial infection. BRAF is a positive regulator of T-cell proliferation. The aim of this study was to evaluate for the first time the role of a functional single nucleotide polymorphism (SNP) of the BRAF gene in association to PI and CP.

Methods: A total of 194 individuals referred to the Periodontology Department of Shahid Beheshti Dental School, Tehran, Iran, were divided into three groups: 74 patients in the CP group (39 men and 35 women, with mean age of 48.3 years), 38 patients in the PI group (20 men and 18 women, with mean age of 50.2 years), and 82 patients in the healthy periodontium group (39 men and 43 women, with mean age of 45.4 years). DNA was extracted from fresh blood samples collected from the arm vein of participants and was transferred to KBiosience institute (United Kingdom) for genotyping. χ2 and Kruskal-Wallis tests were conducted using SPSS software v. 19 for statistical analysis (p<0.05).

Results: The allele (C/T) and genotype (CC, CT, TT) frequencies had insignificant differences among the three groups; however, the CC genotype was more prevalent in the healthy condition than in the disease conditions.

Conclusions: The BRAF gene polymorphism (rs10487888) may not be a genetic determinant for increasing the risk of CP and PI among the Iranian population. More studies with more sample size in different populations are necessary for determining the effect of this SNP.
Methemoglobin incites primaquine toxicity through single-electron oxidation and modification
Authors: Balaji S.N. , Trivedi Vishal
Published: February 2013

Background: Primaquine (Pq) metabolic products are responsible for drug-associated hemotoxicity and limit primaquine usage.

Methods: Methemoglobin (MetHb)-Pq molecular modeling was used to identify the Pq binding pocket. UPLC, mass spectrometry, and other indirect analytical methods were used to predict the metabolite. MetHb generation, development of oxidative stress, inhibition of antioxidant enzymes, and scanning electron microscope (SEM) were used to characterize the hemotoxic potentials of oxidized Pq (Pqox).

Results: MetHb binded Pq at the heme site with K

D
=6.4 μM as evidenced by a difference spectroscopy study. MetHb oxidized Pq through a single e-transfer mechanism to form Pqox. The analysis of Pq from MetHb-H2O2 peroxidase reaction mixture gave peaks at m/z 300.53 and m/z 243.42, corresponding to the hydroxyl and desamino derivative of Pq, respectively. Similar peaks were absent in Pq or Pq incubated with H2O2 in the same buffer system. A robust increase in MetHb formation, reactive oxygen species generation, and inhibition of antioxidant enzymes were found in red blood cells (RBCs) exposed to Pqox compared with a parent drug molecule. The RBC membrane exhibited visible damages to plasma membrane (holes) as evidenced by SEM analysis of Pqox-exposed RBCs.

Conclusions: The MetHb-H2O2 system transforms quiescent parent drug molecule to a highly reactive oxidative form to exhibit severe hemolysis. MetHb-H2O2-mediated Pq hemolytic potentiation that is sensitive to spin trap indicates the role of Pq* radical or other single e-species in the process. The result suggests that MetHb incites the molecular property of the Pq and peroxidase inhibitors can be explored to control drug-associated toxicity.
Effect of stitch and biaxial yarn types on the impact properties of biaxial weft knitted textile composites
Authors: Demircan Ozgur , Kosui Tatsuya , Ashibe Shinsuke , Hamada Yohji , Nakai Asami
Published: February 2013

Within the scope of experiments, the effects of stitch yarn type, such as aramid, glass, and nylon, and biaxial, warp, and weft yarn type, such as aramid and glass, on biaxial weft knitted (BWK) composites were investigated. Five different types of composite panel, which include fiber contents, such as glass-glass-glass, glass-glass-nylon, glass-glass-aramid, aramid-glass-aramid, and aramid-aramid-aramid, were fabricated by hand lay-up method. After the production of composite panels, three-point bending impact and plate bending impact tests were conducted on the specimens. Microstructural characterization of the impact-tested materials was performed using an optical microscope. This study shows that composites with BWK preforms consisting of fiber combinations such as glass-glass-aramid had higher plate bending impact and three-point bending impact properties than the other four types of composite structure.
Handedness-Related Cortical Modulation of the Vestibular-Ocular Reflex
Authors: Arshad Qadeer , Nigmatullina Yuliya , Bronstein Adolfo M.
Published: February 2013

Multisensory visuo-vestibular cortical areas are important for spatial orientation and facilitate the control of the brainstem-mediated vestibular ocular reflex (VOR). Despite reports of visual input and cognitive tasks modulating the VOR through cortical control, it is unknown whether higher-order visual stimuli such as bistable perception and attention tasks involving visual imagery have an effect on the VOR. This is a possibility since such stimuli recruit cortical areas overlapping with those engaged during vestibular activation. Here we used a novel paradigm in which human subjects view bistable perceptual stimuli or perform complex attention tasks during concurrent vestibular stimulation. Bistable perceptual phenomena and attention tasks asymmetrically modulated the VOR but only if they involved a visuospatial component (e.g., binocular motion rivalry but not color rivalry). Strikingly, the lateralization effect was dependent upon the subjects' handedness, making this report the first behavioral demonstration that vestibular cortical processing is strongly lateralized to the non-dominant hemisphere. Furthermore, we show that perceptual transitions can modulate the dynamics of the vestibular system contingent upon the presence of a spatial component in the perceptual transition stimuli. Both perceptual transitions and attentional tasks are thought to invoke a redirection of spatial attention. We infer that such redirection of spatial attention engages multisensory vestibular cortical areas that modulate low-level vestibular function which, in turn, may contribute to spatial orientation.
Ciliary Neurotrophic Factor Controls Progenitor Migration during Remyelination in the Adult Rodent Brain
Authors: Vernerey Julien , Macchi Magali , Magalon Karine , Cayre Myriam , Durbec Pascale
Published: February 2013

Ciliary neurotrophic factor (CNTF) has been shown to be expressed after brain lesions and in particular after demyelination. Here, we addressed the role of this cytokine in the regulation of neural progenitor migration in the adult rodent brain. Using an acute model of demyelination, we show that CNTF is strongly re-expressed after lesion and is involved in the postlesional mobilization of endogenous progenitors that participate in the myelin regenerative process. We show that CNTF controls the migration of subventricular zone (SVZ)-derived neural progenitors toward the demyelinated corpus callosum. Furthermore, an ectopic source of CNTF in adult healthy brains changes SVZ-derived neural progenitors' migratory behavior that migrate toward the source by activation of the Janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3) pathway. Using variousin vitroassays (Boyden chambers, explants, and video time-lapse imaging), we demonstrate that CNTF controls the directed migration of SVZ-derived progenitors and oligodendrocyte precursors. Altogether, these results demonstrate that in addition to its neuroprotective activity and its role in progenitor survival and maturation, CNTF acts as a chemoattractant and participates in the recruitment of endogenous progenitors during myelin repair.
Vascular Endothelial Cells Mediate Mechanical Stimulation-Induced Enhancement of Endothelin Hyperalgesia via Activation of P2X2/3Receptors on Nociceptors
Authors: Joseph Elizabeth K. , Green Paul G. , Bogen Oliver , Alvarez Pedro , Levine Jon D.
Published: February 2013

Endothelin-1 (ET-1) is unique among a broad range of hyperalgesic agents in that it induces hyperalgesia in rats that is markedly enhanced by repeated mechanical stimulation at the site of administration. Antagonists to the ET-1 receptors, ETAand ETB, attenuated both initial as well as stimulation-induced enhancement of hyperalgesia (SIEH) by endothelin. However, administering antisense oligodeoxynucleotide to attenuate ETAreceptor expression on nociceptors attenuated ET-1 hyperalgesia but had no effect on SIEH, suggesting that this is mediated via a non-neuronal cell. Because vascular endothelial cells are both stretch sensitive and express ETAand ETBreceptors, we tested the hypothesis that SIEH is dependent on endothelial cells by impairing vascular endothelial function with octoxynol-9 administration; this procedure eliminated SIEH without attenuating ET-1 hyperalgesia. A role for protein kinase Cε (PKCε), a second messenger implicated in the induction and maintenance of chronic pain, was explored. Intrathecal antisense for PKCε did not inhibit either ET-1 hyperalgesia or SIEH, suggesting no role for neuronal PKCε; however, administration of a PKCε inhibitor at the site of testing selectively attenuated SIEH. Compatible with endothelial cells releasing ATP in response to mechanical stimulation, P2X2/3receptor antagonists eliminated SIEH. The endothelium also appears to contribute to hyperalgesia in two ergonomic pain models (eccentric exercise and hindlimb vibration) and in a model of endometriosis. We propose that SIEH is produced by an effect of ET-1 on vascular endothelial cells, sensitizing its release of ATP in response to mechanical stimulation; ATP in turn acts at the nociceptor P2X2/3receptor.
Temporal Regulation of Nuclear Factor One Occupancy by Calcineurin/NFAT Governs a Voltage-Sensitive Developmental Switch in Late Maturing Neurons
Authors: Ding Baojin , Wang Wei , Selvakumar Tharakeswari , Xi Hualin Simon , Zhu Hong , Chow Chi-Wing , Horton Jay D. , Gronostajski Richard M. , Kilpatrick Daniel L.
Published: February 2013

Dendrite and synapse development are critical for establishing appropriate neuronal circuits, and disrupted timing of these events can alter neural connectivity. Using microarrays, we have identified a nuclear factor I (NFI)-regulated temporal switch program linked to dendrite formation in developing mouse cerebellar granule neurons (CGNs). NFI function was required for upregulation of many synapse-related genes as well as downregulation of genes expressed in immature CGNs. Chromatin immunoprecipitation analysis revealed that a central feature of this program was temporally regulated NFI occupancy of late-expressed gene promoters. Developing CGNs undergo a hyperpolarizing shift in membrane potential, and depolarization inhibits their dendritic and synaptic maturation via activation of calcineurin (CaN) (Okazawa et al., 2009). Maintaining immature CGNs in a depolarized state blocked NFI temporal occupancy of late-expressed genes and the NFI switch program via activation of the CaN/nuclear factor of activated T-cells, cytoplasmic (NFATc) pathway and promotion of late-gene occupancy by NFATc4, and these mechanisms inhibited dendritogenesis. Conversely, inhibition of the CaN/NFATc pathway in CGNs maturing under physiological nondepolarizing conditions upregulated the NFI switch program, NFI temporal occupancy, and dendrite formation. NFATc4 occupied the promoters of late-expressed NFI program genes in immature mouse cerebellum, and its binding was temporally downregulated with development. Further, NFI temporal binding and switch gene expression were upregulated in the developing cerebellum ofNfatc4(−/−) mice. These findings define a novel NFI switch and temporal occupancy program that forms a critical link between membrane potential/CaN and dendritic maturation in CGNs. CaN inhibits the program and NFI occupancy in immature CGNs by promoting NFATc4 binding to late-expressed genes. As maturing CGNs become more hyperpolarized, NFATc4 binding declines leading to onset of NFI temporal binding and the NFI switch program.
State-Dependent Perceptual Learning
Authors: Freyer Frank , Becker Robert , Dinse Hubert R. , Ritter Petra
Published: February 2013

Learning constitutes a fundamental property of the human brain—yet an unresolved puzzle is the profound variability of the learning success between individuals. Here we highlight the relevance of individual ongoing brain states as sources of the learning variability in exposure-based somatosensory perceptual learning. Electroencephalogram recordings of ongoing rhythmic brain activity before and during learning revealed that prelearning parietal alpha oscillations as well as during-learning stimulus-induced contralateral central alpha changes are predictive for the learning outcome. These two distinct alpha rhythm sources predicted up to 64% of the observed learning variability, one source representing an idling state with posteroparietal focus and a potential link to the default mode network, the other representing the sensorimotor mu rhythm, whose desynchronization is indicative for the degree of engagement of sensorimotor neuronal populations during application of the learning stimuli. Unspecific effects due to global shifts of attention or vigilance do not explain our observations. Our study thus suggests a brain state-dependency of perceptual learning success in humans opening new avenues for supportive learning tools in the clinical and educational realms.
Synaptic Cooperativity Regulates Persistent Network Activity in Neocortex
Authors: Favero Morgana , Castro-Alamancos Manuel A.
Published: February 2013

During behavioral quiescence, the neocortex generates spontaneous slow oscillations, which may consist of up-states and down-states. Up-states are short epochs of persistent activity that resemble the activated neocortex during arousal and cognition. Neural activity in neocortical pathways can trigger up-states, but the variables that control their occurrence are poorly understood. We used thalamocortical slices from adult mice to explore the role of thalamocortical and intracortical synaptic cooperativity (the number of coincident afferents) in driving up-states. Cooperativity was adjusted by varying the intensity of electrical or blue-light stimuli in pathways that express channelrhodopsin-2. We found that optogenetics greatly improves the study of thalamocortical pathways in slices because it produces thalamocortical responses that resemble those observedin vivo. The results indicate that more synaptic cooperativity, caused by either thalamocortical or intracortical fast AMPA-receptor excitation, leads to more robust inhibition of up-states because it drives stronger feedforward inhibition. Conversely, during strong synaptic cooperativity that suppresses up-states, blocking fast excitation, and as a result the feedforward inhibition it drives, unmasks up-states entirely mediated by slow NMDA-receptor excitation. Regardless of the pathway's origin, cooperativity mediated by fast excitation is inversely related to the ability of excitatory synaptic pathways to trigger up-states in neocortex.
Telocytes: ultrastructural, immunohistochemical and electrophysiological characteristics in human myometrium
Authors: Cretoiu Sanda M , Cretoiu Dragos , Marin Adela , Radu Beatrice Mihaela , Popescu Laurentiu M
Published: February 2013

Telocytes (TCs) have been described in various organs and species (www.telocytes.com) as cells with telopodes (Tps) – very long cellular extensions with an alternation of thin segments (podomers) and dilated portions (podoms). We examined TCs using electron microscopy (EM), immunohistochemistry (IHC), immunofluorescence (IF), time-lapse videomicroscopy and whole-cell patch voltage clamp. EM showed a three-dimensional network of dichotomous-branching Tps, a labyrinthine system with homocellular and heterocellular junctions. Tps release extracellular vesicles (mean diameter of 160.6±6.9 nm in non-pregnant myometrium and 171.6±4.6 nm in pregnant myometrium), sending macromolecular signals to neighbouring cells. Comparative measurements (non-pregnant and pregnant myometrium) of podomer thickness revealed values of 81.94±1.77 vs 75.53±1.81 nm, while the podoms' diameters were 268.6±8.27 vs 316.38±17.56 nm. IHC as well as IF revealed double c-kit and CD34 positive results. Time-lapse videomicroscopy of cell culture showed dynamic interactions between Tps and myocytes. In non-pregnant myometrium, patch-clamp recordings of TCs revealed a hyperpolarisation-activated chloride inward current with calcium dependence and the absence of L-type calcium channels. TCs seem to have no excitable properties similar to the surrounding smooth muscle cells (SMCs). In conclusion, this study shows the presence of TCs as a distinct cell type in human non-pregnant and pregnant myometrium and describes morphometric differences between the two physiological states. In addition, we provide a preliminaryin vitroelectrophysiological evaluation of the non-pregnant state, suggesting that TCs could influence timing of the contractile activity of SMCs.
Mesenchymal stem cells from amnion and amniotic fluid in the bovine
Authors: Corradetti B , Meucci A , Bizzaro D , Cremonesi F , Lange Consiglio A
Published: February 2013

Amnion and amniotic fluid (AF) are noncontroversial and inexhaustible sources of mesenchymal stem cells (MSCs) that can be harvested noninvasively at low cost. As in humans, also in veterinary field, presumptive stem cells derived from these tissues reveal as promising candidates for disease treatment, specifically for their plasticity, their reduced immunogenicity, and high anti-inflammatory potential. The aim of this work is to obtain and characterize, for the first time in bovine species, presumptive MSCs from the epithelial portion of the amnion (AECs) and from the AF (AF-MSCs) to be used for clinical applications. AECs display a polygonal morphology, whereas AF-MSCs exhibit a fibroblastic-like morphology only starting from the second passage, being heterogeneous during the primary culture. For both lines, the proliferative ability has been found constant over the ten passages studied and AECs show a statistically lower (P<0.05) doubling time with respect to AF-MSCs. AECs express MSC-specific markers (ITGB1(CD29),CD44,ALCAM(CD166),ENG(CD105), andNT5E(CD73)) from P1 to P3; in AF-MSCs, onlyITGB1,CD44, andALCAMmRNAs are detected;NT5Eis expressed from P2 andENGhas not been found at any passage. AF-MSCs and AECs are positive for the pluripotent markers (POU5F1(OCT4) andMYC(c-Myc)) and lack of the hematopoietic markers. When appropriately induced, both cell lines are capable of differentiating into ectodermal and mesodermal lineages. This study contributes to reinforce the emerging importance of these cells as ideal tools in veterinary medicine. A deeper evaluation of the immunological properties needs to be performed in order to better understand their role in cellular therapy.
Evaluation of mercury and lead content in the liver of the cormorant (Phalacrocorax carbo sinensis) population of Kis-Balaton, Hungary
Authors: Lehel József , Gál János , Faragó Sándor , Berta Erzsébet , Andrásofszky Emese , Fekete Sándor , Mándoki Míra , Budai Péter , Kormos Éva , Marosán Miklós
Published: February 2013

Mercury and lead concentrations were measured in the livers of cormorant (Phalacrocorax carbo sinensis), an aquatic bird species living and nesting in the special, highly protected nature conservation area of Kis-Balaton, Hungary. The measurements of metal concentrations were performed by atomic absorption spectrometry using the cold vapour method for mercury and the electrothermal method for lead. Mercury concentrations in the livers were significantly higher in the adult population (4.479 ± 3.336 mg/kg dry matter, DM) than in the juvenile birds (2.682 ± 2.087 mg/kg DM), indicating an increase of bioaccumulation with age. A similar pattern was not observed for lead. There were no statistical differences between males and females either in mercury or in lead concentrations. The average levels of mercury (3.580 ± 2.906 mg/kg DM) and lead (0.746 ± 0.499 mg/kg DM) were statistically different in the liver. No correlation was found between the concentrations of the two heavy metals. Recently, the wild birds have been chronically exposed to subtoxic amounts of metals which have a tendency to accumulate especially in the soft tissues.
Effects of bovine viral diarrhoea virus on the fertility of cows
Authors: Yavru Sibel , Kale Mehmet , Gulay Mehmet , Yapici Orhan , Bulut Oya , Ata Ayhan
Published: February 2013

The aim of the present study was to determine the possible relationship between bovine viral diarrhoea (BVD) virus infection and the appearance of cervical mucous discharge (CMD) and the reproductive performance of cows in oestrus. For this purpose, CMD from 97 Holstein cows in oestrus was evaluated visually before artificial insemination (AI). Cows in oestrus were inseminated with frozen semen free from BVD virus (BVDV). Blood samples were tested by enzyme-linked immunoassay (ELISA) for antigen (Ag) and antibodies (Ab) of BVDV. The presence of the BVDV genome in cervical mucus samples was tested by reverse transcriptase-polymerase chain reaction (RT-PCR). The presence of BVDV Ab, Ag or genome was not associated with abnormal cervical mucous discharge (A-CMD). However, the presence of BVDV Ag (but not of the BVDV Ab) in blood samples was associated with a lower first service conception rate (FSCR; 27.8 vs. 70.9%; P < 0.01), indicating that BVDV viraemia at the time of AI has a negative effect on the fertility of cows.
Value of semen parameters, with special reference to TNF-α, in predicting the quality of boar semen after short-term storage
Authors: Mrkun Janko , Kosec Marjan , Zrimšek Petra
Published: February 2013

The aim of this study was to address the question whether changes in boar semen quality after short-term storage could be predicted on the basis of standard semen parameters and TNF-α level determined on the day of semen collection under commercial conditions. Progressive motility showed the highest positive correlation with morphology on day 0 of collection, and progressive motility on day 3 (P < 0.05) showed a negative correlation with acrosome abnormalities (P < 0.05). According to the area under receiver operating characteristics (ROC) curves (AUCs), progressive motility could also be used in predicting semen quality after 3 days of storage (AUC > 0.5; P < 0.05). TNF-α in seminal plasma is the only parameter measured on day 0 to show a significant correlation with the percentage of viable spermatozoa after 3 days of semen storage (r = 0.495, P < 0.05). ROC analysis shows that TNF-α level is helpful in discriminating viability outcome after semen storage (AUC = 0.94, P < 0.001). We can predict with 92.35% certainty that fresh semen samples with more than 150 pg/ml of TNF-α in the seminal plasma will retain more than 85% of viable spermatozoa after 3 days of storage. Thus, TNF-α can contribute to predicting the quality of short-term stored semen.