bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross-hybridization modeling on Affymetrix exon arrays
Authors: Kapur Karen , Jiang Hui , Xing Yi , Wong Wing Hung
Published: November 2008

Motivation: Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.

Results: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for cross-hybridization biases of gene-level expression estimates. Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improve-ment of gene expression estimates.

Availability: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/.

Contact:  whwong@stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
Authors: Milne Iain , Lindner Dominik , Bayer Micha , Husmeier Dirk , McGuire Gráinne , Marshall David F. , Wright Frank
Published: November 2008

Summary: TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). Methods available include model selection and phylogenetic tree estimation using the Bayesian inference and maximum likelihood (ML) approaches, in addition to recombination detection methods. The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from ML co-estimation of the tree and the substitution model. Phylogenetic software available includes PhyML, RAxML and MrBayes.

Availability: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.

Contact:  iain.milne@scri.ac.uk
TheArabidopsisGRAS Protein SCL14 Interacts with Class II TGA Transcription Factors and Is Essential for the Activation of Stress-Inducible Promoters
Authors: Fode Benjamin , Siemsen Tanja , Thurow Corinna , Weigel Ralf , Gatz Christiane
Published: November 2008

The plant signaling molecule salicylic acid (SA) and/or xenobiotic chemicals like the auxin mimic 2,4-D induce transcriptional activation of defense- and stress-related genes that contain activation sequence-1 (as-1)–like cis-elements in their promoters. as-1–like sequences are recognized by basic/leucine zipper transcription factors of the TGA family. Expression of genes related to the SA-dependent defense program systemic acquired resistance requires the TGA-interacting protein NPR1. However, a number of as-1–containing promoters can be activated independently from NPR1. Here, we report the identification of Arabidopsis thaliana SCARECROW-like 14 (SCL14), a member of the GRAS family of regulatory proteins, as a TGA-interacting protein that is required for the activation of TGA-dependent but NPR1-independent SA- and 2,4-D–inducible promoters. Chromatin immunoprecipitation experiments revealed that class II TGA factors TGA2, TGA5, and/or TGA6 are needed to recruit SCL14 to promoters of selected SCL14 target genes identified by whole-genome transcript profiling experiments. The coding regions and the expression profiles of the SCL14-dependent genes imply that they might be involved in the detoxification of xenobiotics and possibly endogenous harmful metabolites. Consistently, plants ectopically expressing SCL14 showed increased tolerance to toxic doses of the chemicals isonicotinic acid and 2,4,6-triiodobenzoic acid, whereas the scl14 and the tga2 tga5 tga6 mutants were more susceptible. Hence, the TGA/SCL14 complex seems to be involved in the activation of a general broad-spectrum detoxification network upon challenge of plants with xenobiotics.
Morphology and sedimentary systems in the Central Bransfield Basin, Antarctic Peninsula: sedimentary dynamics from shelf to basin
Authors: García Marga , Ercilla Gemma , Alonso Belén
Published: November 2008

A detailed regional characterization of the physiography, morphology and sedimentary systems of the Central Bransfield Basin (CBB) was carried out using swath bathymetry and high‐ and very high‐resolution seismic profiles. The basin margins show continental shelves with numerous glacial troughs, and continental slopes where relatively wide and flat slope platforms represent the middle domain in an atypical physiographic scenario in glaciated margins. Although the CBB is tectonically active, most of the morphologic features are sedimentary in origin, and can be classified into four sedimentary systems: (1) glacial‐glaciomarine, composed of erosional surfaces, glacial troughs, furrows and draping sheets; (2) slope‐basin, formed by trough mouth fans, slope aprons, the Gebra‐Magia instability complex and turbidity systems; (3) seabed fluid outflow system composed of pockmark fields; and (4) contourite, composed of drifts and moats. The sedimentary systems show a clear zonation from shelf to basin and their dynamics reflects the complex interplay among glacial, glaciomarine, marine and oceanographic processes involved in the entire shelf‐to‐basin sediment distribution. The CBB morphology is primarily controlled by glacial/interglacial cyclicity and physiography and to a lesser extent by tectonics and oceanography. These factors have affected the South Shetland Islands (SSI) and Antarctic Peninsula (AP) margins differently, creating a relatively starved SSI margin and a more constructional AP margin. They have also created two entire sediment‐dispersal domains: the shelf‐to‐slope, which records the glaciation history of the CBB; and the lower slope‐to‐basin, which records the imprint of local factors. This study provides a ‘source‐to‐sink’ sedimentary scheme for glaciated margins, which may be applied to the basin research in other margins, based on the characterization of sedimentary systems, their boundaries and the linkages among them. This approach proves to be adequate for the identification of global and local factors governing the CBB and may therefore be applied to other study areas.
Adolescent smoking and health‐related behaviours: interrelations in a Greek school‐based sample
Authors: Giannakopoulos G. , Panagiotakos D. , Mihas C. , Tountas Y.
Published: November 2008

Background  Although several studies have reported findings concerning the interrelationship between smoking and specific health behaviours, little research has investigated how smoking behaviour may be associated with a cluster of health‐related behaviours. The present study was an effort to extend previous research through assessing smoking status, patterns of physical and sedentary activity, as well as eating behaviours and diet quality, in order to gain some insight regarding the relationship between cigarette smoking and a cluster of health behaviours in a Greek sample of adolescents.

Methods  A sample of 2008 students (1021 male and 987 female, 12–17 years of age, 7th–12th grade) was selected from all schools of a representative Athens suburb in Greece. All children completed a questionnaire that was developed for the purposes of the study which retrieved information about age, sex, school class, individual and family smoking status, dietary habits and physical activity. Various statistical tests were performed.

Results  Age, playtime, consumption of soft drinks and foods from school canteens were positively associated with smoking status while the consumption of fruit juice, dairy products for breakfast and the frequency of breakfasts were inversely associated the aforementioned dependent variable.

Conclusions  This study supports the interrelationships between multiple lifestyle behaviours and tobacco use in adolescents. Future research is needed in order to elaborate on the nature of these relations, especially for those at higher risk.
Children's specific fears
Authors: Meltzer H. , Vostanis P. , Dogra N. , Doos L. , Ford T. , Goodman R.
Published: November 2008

Background  Most children experience some degree of fear during their development. Specific fears are considered as an appropriate response provided that they are proportionate to the intensity of the perceived threat. Our aim is to present the prevalence of specific fears among children in the Great Britain, their socio‐demographic correlates, in particular their association with ethnicity.

Methods  Data on the child's experience of specific fears were obtained from parents of a national representative sample of 5‐ to 16‐year‐olds using the Development and Well‐Being Assessment. Biographic, socio‐demographic and socioeconomic characteristics of the child and the family were included in the questionnaire.

Results  About one‐third of children were assessed by their parents as having at least one of 12 specific fears. The most commonly reported fears were animals (11.6%), blood/injections (10.8%) and the dark (6.3%). Just less than 1% of all children were assessed according to International Classification of Diseases research diagnostic criteria as having a specific phobia. Biographic, socio‐demographic and socioeconomic factors were independently associated with a greater likelihood of a child having particular fears. The most marked associations were fears of the dark, loud noises, imagined supernatural beings in younger children and fear of animals among girls and all non‐white groups.

Conclusions  Although fears are only labelled as phobias when they impair functioning and interfere with life, they can cause personal distress to children and also can interfere with their daily activities. Children's fears differ in nature across different ethnic groups. Culturally mediated beliefs, values and traditions may play a role in their expression.
Non-response to infliximab may be due to innate neutralizing anti-tumour necrosis factor-α antibodies
Authors: Ebert E C , Das K M , Mehta V , Rezac C
Published: November 2008

Infliximab is a chimeric anti-tumour necrosis factor (TNF)-α antibody that is therapeutic in many patients with inflammatory bowel disease. What causes certain patients not to respond is unknown. The question posed is whether innate anti-TNF-α antibodies play any role in the response to infliximab. Blood was drawn prior to the initial dose of infliximab. Serum anti-TNF-α antibodies were quantitated by enzyme-linked immunosorbent assay (ELISA). Affinity-purified anti-TNF-α antibodies were isolated from serum immunoglobulin G using TNF-α-coated beads. The ability of these antibodies to induce apoptosis of macrophages was measured by annexin and propidium iodide staining. Changes in TNF receptor type 2 (TNFR2) expression and release were determined by immunofluorescence and ELISA respectively. TNF-α-neutralization was assessed by the reversal of the lytic actions of TNF-α on WEHI cells. The amounts of innate anti-TNF-α antibodies in the serum from infliximab responders versus non-responders were the same. Apoptosis of monocytes increased with infliximab and by several of the purified anti-TNF-α antibodies, but these findings did not vary with the patients' responses to infliximab. Effects of the anti-TNF-α antibodies on the expression of TNFR2 on monocytes and their release of soluble TNFR2 did not vary with the patients' responses to infliximab. However, the neutralizing capacity of these antibodies differed, with responders having antibodies that reduced only 47 ± 4% of the TNF-α activity while those from non-responders reduced 70 ± 5% of the TNF-α activity (P < 0·01). Non-responders have innate anti-TNF-α antibodies with greater neutralizing activity than antibodies from responders. Any TNF-α-mediated disease process would be neutralized by intrinsic antibodies, so that the disease is likely to be driven by non-TNF-α-mediated events.
Expression of a B‐cell‐restricted isoform of CD45 is associated with maturity in rat serosal and connective‐tissue mast cells
Authors: Yu Chunping , Moghaddami Mahin , Mayrhofer Graham
Published: November 2008

A number of technical limitations make differential staining with dyes such as Alcian blue and Safranin O unsatisfactory as the primary method for assessing the maturity of connective tissue mast cells in rodents. We demonstrated for the first time that in the steady state, most serosal mast cells in normal rats express a high‐molecular‐weight isoform of CD45 that reacts with monoclonal antibody OX33 (OX33+) and has been reported previously only on B cells. However, a small proportion did not express this isoform (OX33−) and this subset predominated during the early stages of mast cell regeneration in the peritoneal cavity. Furthermore, there was a progressive increase in the proportion of donor‐derived OX33+ cells after intraperitoneal adoptive transfer of purified OX33− mast cells to CD45 congenic recipients. These results indicate that serosal mast cells up‐regulate expression of the OX33‐reactive CD45 isoform(s) as they mature. Interestingly, acquisition of OX33‐reactive CD45 did not correlate temporally with sulphation of glycosaminglycan in the mast cell granules. Expression of this isoform was used also to assess the maturity of connective tissue mast cells during mastocytosis in synovium associated with T‐cell‐mediated experimental polyarthritis. Together, our results demonstrate that OX33‐reactive CD45 is a marker that can be used to assess the maturity of serosal and connective tissue mast cells during normal homeostasis and during pathological processes. The significance of differential expression of CD45 isoforms may be to regulate the sensitivity of maturing mast cells to the actions of growth factors and activating stimuli.
A chromatic explosion: the development and future of multiparameter flow cytometry
Authors: Chattopadhyay Pratip K. , Hogerkorp Carl‐Magnus , Roederer Mario
Published: November 2008

Multiparameter flow cytometry has matured tremendously since the 1990s, giving rise to a technology that allows us to study the immune system in unprecedented detail. In this article, we review the development of hardware, reagents, and data analysis tools for multiparameter flow cytometry and discuss future advances in the field. Finally, we highlight new applications that use this technology to reveal previously unappreciated aspects of cell biology and immunity.
Increased glial‐derived neurotrophic factor in the small intestine of rats infected with the tapeworm, Hymenolepis diminuta
Authors: Starke‐Buzetti Wilma Aparecida , Oaks John A.
Published: November 2008

The neurotrophin, glial‐derived neurotrophic factor (GDNF), is essential for the development of the enteric nervous system (ENS) in both the embryo and neonate and may be important for maintenance and plasticity of ENS. The tapeworm, Hymenolepis diminuta, altered the number of cells containing GNDF in the host’s jejunum and ileum. Numbers and locations of GDNF‐containing cells were determined by applying monoclonal anti‐GDNF antibody to intestinal segments collected from infected and uninfected age‐matched rats during the initial 34 days post‐infection (dpi). Most cells staining positive for GDNF were present in the lamina propria of the jejunum and ileum from both infected and uninfected rats. The co‐localization of staining by the antibodies, anti‐GDNF and anti‐ED2 (a nuclear specific antibody for resident macrophages) indicated that at least 74% of the cells staining for GDNF were macrophages. Mast cells did not stain with the anti‐GDNF antibody. The increased number of GDNF+ cells in the infected rat intestine suggests that this neurotrophin may play a role in the neural and mucosal responses to lumenal tapeworm infection.
An intravital microscopic study of the hepatic microcirculation in cirrhotic mice models: relationship between fibrosis and angiogenesis
Authors: Vanheule Eline , Geerts Anja M. , Van Huysse Jacques , Schelfhout Daphné , Praet Marleen , Van Vlierberghe Hans , De Vos Martine , Colle Isabelle
Published: November 2008

This intravital fluorescence microscopy (IVFM) study validates cirrhotic mice models and describes the different intrahepatic alterations and the role of angiogenesis in the liver during genesis of cirrhosis. Cirrhosis was induced by subcutaneous injection of carbon tetrachloride (CCl4) and by common bile duct ligation (CBDL) in mice. Diameters of sinusoids, portal venules (PV), central venules (CV) and shunts were measured at different time points by IVFM. Thereafter, liver samples were taken for sirius red, CD31, Ki67, vascular endothelial growth factor (VEGF) and α‐smooth muscle actin (α‐SMA) evaluation by immunohistochemistry (IHC). In parallel with fibrogenesis, hepatic microcirculation was markedly disturbed in CCl4 and CBDL mice with a significant decrease in sinusoidal diameter compared to control mice. In CCl4 mice, CV were enlarged, with marked sinusoidal‐free spaces around CV. In contrast, PV were enlarged in CBDL mice and bile lakes were observed. In both mice models, intrahepatic shunts developed gradually after induction. During genesis of cirrhosis using CD31 IHC we observed a progressive increase in the number of blood vessels within the fibrotic septa area and a progressively increase in staining by Ki67, VEGF and α‐SMA of endothelial cells, hepatocytes and hepatic stellate cells respectively. In vivo study of the hepatic microcirculation demonstrated a totally disturbed intrahepatic architecture, with narrowing of sinusoids in both cirrhotic mice models. The diameters of CV and PV increased and large shunts, bypassing the sinusoids, were seen after both CCl4 and CBDL induction. Thus present study shows that there is angiogenesis in the liver during cirrhogenesis, and this is probably due partially to an increased production of VEGF.
Matrix metalloproteinase‐9 contributes to intestinal tumourigenesis in the adenomatous polyposis coli multiple intestinal neoplasia mouse
Authors: Sinnamon Mark J. , Carter Kathy J. , Fingleton Barbara , Matrisian Lynn M.
Published: November 2008

Matrix metalloproteinases (MMPs) are a family of 23 extracellular proteases that are best known for their collective ability to degrade all components of the extracellular matrix. We previously demonstrated that genetic ablation of MMP‐7 reduced tumour multiplicity in multiple intestinal neoplasia (Min) mice possessing a genetic alteration in the adenomatous polyposis coli gene (APC). These mice, commonly referred to as APC‐Min mice, are a frequently used model of early intestinal tumourigenesis. To examine further the role of MMPs in intestinal tumour development, we generated APC‐Min mice genetically deficient in MMP‐2, ‐9, ‐12 or ‐19. Genetic ablation of MMP‐2, ‐12 or ‐19 did not affect multiplicity or size of intestinal tumours when crossed into the APC‐Min system. However, MMP‐9 deficient animals developed 40% fewer tumours than littermate controls, although tumour size distribution remained unaffected. Intestinal adenomas from MMP‐9 deficient mice demonstrated a 50% decrease in proliferating cells compared with control tissues, with no difference in apoptosis. To determine the cellular origin of MMP‐9 in these tumours, immunofluorescent co‐staining with markers for different leucocyte lineages was used to demonstrate that intratumoural MMP‐9 is largely a product of neutrophils. These studies extend the potential targets for chemoprevention of intestinal adenomas to MMP‐9 in addition to MMP‐7 and exclude MMP‐2,‐12,‐19 as attractive targets for intervention.
A rough guide to the non‐coding RNA world of Salmonella
Authors: Vogel Jörg
Published: November 2008

Salmonella species are enterobacterial pathogens that have been exceptionally well investigated with respect to virulence mechanisms, microbial pathogenesis, genome evolution and many fundamental pathways of gene expression and metabolism. While these studies have traditionally focused on protein functions, Salmonella has also become a model organism for RNA‐mediated regulation. The present review is dedicated to the non‐coding RNA world of Salmonella: it covers small RNAs (sRNAs) that act as post‐transcriptional regulators of gene expression, novel Salmonella cis‐regulatory RNA elements that sense metabolite and metal ion concentrations (or temperature), and globally acting RNA‐binding proteins such as CsrA or Hfq (inactivation of which cause drastic phenotypes and virulence defects). Owing to mosaic genome structure, some of the Salmonella sRNAs are widely conserved in bacteria whereas others are very specific to Salmonella species. Intriguingly, sRNAs of either type (CsrB/C, InvR, SgrS) facilitate cross‐talk between the Salmonella core genome and its laterally acquired virulence regions. Work in Salmonella also identified physiological functions (and mechanisms thereof) of RNA that had remained unknown in Escherichia coli, and pioneered the use of high‐throughput sequencing technology to identify the sRNA and mRNA targets of bacterial RNA‐binding proteins.
TBP domain symmetry in basal and activated archaeal transcription
Authors: Ouhammouch Mohamed , Hausner Winfried , Geiduschek E. Peter
Published: November 2008

The TATA box binding protein (TBP) is the platform for assembly of archaeal and eukaryotic transcription preinitiation complexes. Ancestral gene duplication and fusion events have produced the saddle‐shaped TBP molecule, with its two direct‐repeat subdomains and pseudo‐two‐fold symmetry. Collectively, eukaryotic TBPs have diverged from their present‐day archaeal counterparts, which remain highly symmetrical. The similarity of the N‐ and C‐halves of archaeal TBPs is especially pronounced in the Methanococcales and Thermoplasmatales, including complete conservation of their N‐ and C‐terminal stirrups; along with helix H′1, the C‐terminal stirrup of TBP forms the main interface with TFB/TFIIB. Here, we show that, in stark contrast to its eukaryotic counterparts, multiple substitutions in the C‐terminal stirrup of Methanocaldococcus jannaschii (Mja) TBP do not completely abrogate basal transcription. Using DNA affinity cleavage, we show that, by assembling TFB through its conserved N‐terminal stirrup, Mja TBP is in effect ambidextrous with regard to basal transcription. In contrast, substitutions in either its N‐ or the C‐terminal stirrup abrogate activated transcription in response to the Lrp‐family transcriptional activator Ptr2.
Modelling of malaria temporal variations in Iran
Authors: Haghdoost Ali‐Akbar , Alexander Neal , Cox Jonathan
Published: November 2008

Objective  To model the temporal variations in malaria episodes in a hypo‐endemic area of Iran and to assess the feasibility of an epidemic early warning system.

Methods and Materials  Malaria episode data for Kahnooj District, south‐east Iran, were collected from the local health system for the period 1994–2002. Plasmodium species‐specific models were generated using Poisson regression. Starting with a simple model which included only temporal effects, we iteratively added more explanatory variables to maximize goodness of fit.

Results  Of 18 268 recorded malaria episodes, more than 67% were due to P. vivax. In addition to seasonality and secular trend, we found that incorporating a 1‐month time lag between key meteorological variables and the predicted number of cases maximized goodness of fit. Maximum temperature, mean relative humidity and previous numbers of malaria cases were the most important predictors. These were included in the model with lags of no less than three dekads, i.e. three 10‐day periods or effectively 1 month.

Conclusion  Simple models based on climatic factors and information on past case numbers may be useful in improving the quality of the malaria control programme in Iran, particularly in terms of assuring accurate targeting of interventions in time and space. The models developed in this study are based on explanatory data that incorporate a lag of 1 month (i.e. data that were recorded 21–50 days previously). In practice, this translates into an operational ‘window’ of 1 month. Provided appropriate modes of data exchange exist between key stakeholders and appropriate systems for operational response are in place, this type of early warning information has the potential to lead to significant reductions in malaria morbidity in Iran.
GTPγS antagonizes the mastoparan‐induced in vitro activity of PIP2‐phospholipase C from symbiotic root nodules of Phaseolus vulgaris
Authors: De Los Santos‐Briones César , Cárdenas Luis , Estrada‐Navarrete Georgina , Santana Olivia , Minero‐García Yereni , Quinto Carmen , Sánchez Federico
Published: November 2008

Phospholipase C (PLC) has been suggested to have a role in signal perception by Nod factors (NFs) in legume root hair cells. For instance, mastoparan, a well‐described agonist of heterotrimeric G protein, induces nodulin expression after NFs treatment or Rhizobium inoculation. Furthermore, it has been recently demonstrated that mastoparan also mimics calcium oscillations induced by NFs, suggesting that PLC could play a key role during the nodulation process. In this study, we elucidate a biochemical relationship between PLC and heterotrimeric G proteins during NFs signaling in legumes. In particular, the effect of NFs on in vitro PLC activity from nodule membrane fractions in the presence of guanosine 5′‐[γ‐thio]triphosphate (GTPγS) and mastoparan was assayed. Our results indicate that for phosphatidylinositol 4,5 bisphosphate (PIP2)‐PLC, there is a specific activity of 20–27 nmol mg−1 min−1 in membrane fractions of nodules 18–20 days after inoculation with Rhizobium tropici. Interestingly, in the presence of 5 μM mastoparan, PIP2‐PLC activity was almost double the basal level. In contrast, PIP2‐PLC activity was downregulated by 1–10 μM GTPγS. Also, PLC activity was decreased by up to 64% in the presence of increasing concentrations of NFs (10−8 to 10−5 M). NFs are critical signaling molecules in rhizobia/legume symbiosis that can activate many of the plant’s early responses during nodule development. Calcium spiking, kinases, PLC activity and possibly G proteins appear to be components downstream of the NFs perception pathway. Our results suggest the occurrence of a dual signaling pathway that could involve both G proteins and PLC in Phaseolus vulgaris during the development of root nodules.
Patterns of ion excretion and survival in two stoloniferous arid zone grasses
Authors: Naz Nargis , Hameed Mansoor , Wahid Abdul , Arshad Muhammad , Aqeel Ahmad Muhammad Sajid
Published: November 2008

Desert plants show specific mechanisms to thrive under prevailing harsh conditions. To study the survival mechanism(s) in native desert plant species, Lesser Cholistan desert in Pakistan was surveyed and two potential salt secretory grass species, Aeluropus lagopoides and Ochthochloa compressa, were selected from five saline sites. Both these grasses responded differentially to saline environments by showing specialized mechanisms of survival including excretion of toxic ions through trichomes, vesicular and glandular hairs through leaf surface. In A. lagopoides, salt tolerance was associated with excreted Na+ concentration through leaf surface and accumulation of useful ions like Ca2+ and K+ in the shoot. Contrarily, O. compressa excreted all the ions through leaves without discriminating among toxic or beneficial ions. Results suggested that A. lagopoides was more successfully adapted to saline desert environments than O. compressa by excretion of excessive toxic ions and retention of Ca2+ and K+ in the shoot. This appears to be an adaptive character of the former species to successfully thrive in harsh desert conditions.
Factors Affecting Plasma Pregnancy‐associated Glycoprotein 1 Concentrations Throughout Gestation in High‐producing Dairy Cows
Authors: Serrano B , López‐Gatius F , Santolaria P , Almería S , García‐Ispierto I , Bech‐Sabat G , Sulon J , De Sousa NM , Beckers JF , Yániz JL
Published: November 2008

Contents

This study was designed to establish the factors, if any, which could affect plasma pregnancy‐associated glycoprotein‐1 (PAG‐1) expression in a study population of 87 pregnant, high‐producing dairy cows. The factors examined were: semen providing breed (Holstein‐Friesian vs Limousin), outcome of gestation (male vs female newborn, and singleton vs twin pregnancies), lactation number, milk production at pregnancy diagnosis, plasma progesterone concentration, season of gestation (warm period, March–November vs cool period, December–February), and day of gestation (40, 90, 120, 150, 180 and 210). Pregnancy was diagnosed by transrectal ultrasound on day 40 post‐insemination and by palpation per rectum on days 90, 120, 150, 180 and 210. Blood samples were collected from each animal immediately before each pregnancy diagnosis. The relative contributions of the different factors on PAG‐1 concentrations were evaluated by GLM repeated measures analysis of variance. No significant effects of the herd, foetal sex, milk production, lactation number and plasma progesterone concentrations were observed. In contrast, twin pregnancy, the use of Limousin semen and conception during the cool period were correlated with significantly increased plasma PAG‐1 concentrations throughout gestation. Our data indicate that both cow well‐being during early placental development, determined in our conditions by reduced heat stress when conception occurred in the cool season, and crossbreed pregnancies lead to improved PAG‐1 production throughout the gestation period.
Identification of Sperm‐Head Morphometric Subpopulations in Iberian Red Deer Epididymal Sperm Samples
Authors: Esteso MC , Fernández‐Santos MR , Soler AJ , Montoro V , Martínez‐Pastor F , Garde JJ
Published: November 2008

Contents

Computer‐assisted sperm morphometry analysis (CASMA) was used in this study to identify sperm morphometric subpopulations in Iberian red deer epididymal sperm samples. Epididymal sperm samples were collected from 37 mature stags and were divided. One portion was diluted in a Tris–citrate–egg yolk medium. A microscope slide was prepared from single extended sperm samples prior to freezing. The remainder of each sample was frozen in nitrogen vapours using a conventional protocol. After thawing, sperm smears were prepared as described for extended samples. All slides were air‐dried and stained with Hemacolor®. The sperm‐head dimensions for a minimum of 145 sperm‐heads were analyzed from each sample by means of the Sperm‐Class Analyser®, and the mean measurements recorded. Each sperm‐head was measured for four primary sperm‐head parameters, and five parameters of head shape. All sperm morphometric parameters evaluated were placed in a statistical database and a multivariate cluster analysis was performed. The clustering analyses, based on 10 867 individual spermatozoa, revealed the existence of three subpopulations (SP1, SP2, SP3) of spermatozoa with different morphometric characteristics (p < 0.001). The proportion of spermatozoa present in any of the three subpopulations remained constant (p > 0.05) through the cryopreservation process. Pre‐freeze and post‐thaw sperm quality wasin vitroevaluated by microscopic assessments of individual sperm motility and of plasma membrane and acrosome integrities. In conclusion, our results show that applying the CASMA techniques and multivariate cluster analyses, it was possible to determine that three subtle subpopulations of spermatozoa with different morphometric characteristics coexist in red deer semen.
Comparative Study between Slow Freezing and Vitrification of Mouse Embryos Using Different Cryoprotectants
Authors: Liu W‐X , Luo M‐J , Huang P , Yue L‐M , Wang L , Zhao C‐Y , He Y‐P , Zhang J‐H , Zheng Y
Published: November 2008

Contents

The objective of this study was to evaluate the effects of different cryoprotectants and different cryopreservation protocols on the development of mouse eight‐cell embryos. Mouse eight‐cell embryos were cryopreserved by using propylene glycerol (PROH), ethylene glycerol (EG), dimethyl sulfoxide (DMSO) or glycerol (G) as cryoprotectant with slow‐freezing or Vit‐Master vitrification protocol. After thawing, the survival rate, blastocyst formation rate and blastocyst hatching rate of the embryos were compared. When the mouse eight‐cell embryos were cryopreserved by the slow‐freezing, the survival rate, the blastocyst formation rate and the blastocyst hatching rate of the embryos with PROH were significantly higher than those of DMSO and G (p < 0.05, respectively), but not significantly different among those of DMSO, G and EG (p > 0.05, respectively), and not significantly different between those of PROH and EG (p > 0.05, respectively). When the mouse eight‐cell embryos were cryopreserved by Vit‐Master vitrification, the survival rate, the blastocyst formation rate and the blastocyst hatching rate of the embryos with EG were significantly higher than those of PROH, DMSO and G (p < 0.05, respectively). Yet, there were no significant differences among those of PROH, DMSO and G (p > 0.05, respectively). In conclusion, PROH was the optimal cryoprotectant for the cryopreservation of mouse eight‐cell embryos by slow‐freezing protocol. EG was the optimal cryoprotectant for the cryopresevation of mouse eight‐cell embryos by Vit‐Master vitrification protocol, which may be commonly used in clinical and laboratory practice.
DNA Status on Thawed Semen from Fighting Bull: A Comparison Between the SCD and the SCSA Tests
Authors: Martínez‐Pastor F , Del Rocío Fernández‐Santos M , Domínguez‐Rebolledo ÁE , Esteso MC , Garde JJ ,   Biology of Reproduction Group
Published: November 2008

Contents

The assessment of sperm chromatin status is compulsory in a complete spermiogram. Here we applied the sperm chromatin structure assay (SCSA) and the sperm chromatin dispersion (SCD) test to assess the chromatin status of three fighting bulls. Cryopreserved semen (two straws/bull) were analysed by duplicate after thawing and after 6 h at 37°C with and without oxidative stress (1 mm FE2+). Results (SCD: percentage of spermatozoa with halo; SCSA: SD‐DFI, %DFI and HDS) were analysed for differences between bulls and treatments, sensitivity and specificity (receiver operating characteristic curves) and repeatability (repeatability coefficients as 2SD of duplicate differences).%DFI for the three bulls was below 2% at 0 h, indicating no risk for fertility according to previous reports. It increased slightly for two of the bulls after FE2+ treatment (%DFI < 5%) and more pronouncedly for the other bull (C, %DFI∼10%), which merits further investigation. SCD rendered higher percentage of halos for bull C, but could not discriminate between samples with and without oxidizing treatment (AUC: 0.52). SCSA (%DFI) showed a high discriminating ability between treatments (AUC: 0.96). The repeatability coefficient was also higher for SCD (5.9) than for %DFI (1.8), indicating lower repeatability for SCD. Overall, %DFI might be the most useful parameter for assessing sperm chromatin on fighting bull. SCD might yield different information than SCSA, hence further research is warranted.
Quality of life and physical functioning in HIV‐infected individuals receiving antiretroviral therapy in KwaZulu‐Natal, South Africa
Authors: McInerney Patricia A. , Ncama Busisiwe P. , Wantland Dean , Bhengu Busisiwe R. , McGibbon Chris , Davis Sheila M. , Corless Inge B. , Nicholas Patrice K.
Published: November 2008

KwaZulu‐Natal province, South Africa, accounts for 28.7% of the HIV infection total and one‐third of infections among youth and children in South Africa. The purpose of this study was to examine the variables of HIV/AIDS symptoms, social support, influence of comorbid medical problems, length of time adhering to antiretroviral therapy medications, quality of life, adherence to antiretroviral medications, and physical functioning in HIV‐infected individuals. Based on our model, the combination of these variables was found to determine physical functioning outcomes and adherence to HIV medications. Significant relationships were observed between physical functioning and the dependent variables of length of time on medications, comorbid health problems, and social support. A linear regression model was built to determine the degree to which these variables predicted physical functioning. In total, these predictor variables explained 29% of the variance in physical functioning. These results indicate that those individuals who reported a greater length of time on medications, fewer comorbid health problems, and greater social support had better physical functioning.
Having knowledge of metabolic syndrome: Does the meaning and consequences of the risk factors influence the life situation of Swedish adults?
Authors: Frisman Gunilla Hollman , Berterö Carina
Published: November 2008

The underlying causes of metabolic syndrome (MS) are uncertain. Knowledge from those who have experience of this syndrome should provide new insight. The aim was to explore the meaning and consequences of MS. Thirteen Swedish adults with MS, aged between 33 and 82 years, were interviewed. The interviews were analyzed using constant comparative analysis, which is the basis of grounded theory. The core category for the meaning and consequences of having the risk factors of MS consisted of the recurrence of behavior. The participants attempted to balance their insight into the causes and consequences by referring to their normal life, lifestyle, and fatalistic approach to life. Attention needs to be paid to the attitudes of the individuals with MS, as well as the known risk factors and their consequences, in order to facilitate a long‐term lifestyle change in these individuals.
Chronic stress‐induced alterations in amygdala responsiveness and behavior – modulation by trait anxiety and corticotropin‐releasing factor systems
Authors: Sandi Carmen , Cordero M. Isabel , Ugolini Annarosa , Varea Emilio , Caberlotto Laura , Large Charles H.
Published: November 2008

The basolateral nucleus of the amygdala (BLA) plays a key role in emotional arousal and anxiety, and expresses high levels of corticotropin‐releasing factor receptor (CRFR)1. In rat brain slices, we have recently shown that afferent activation of the BLA is increased following application of exogenous corticotropin‐releasing factor (CRF). Here we examined the impact of chronic unpredictable stress (CUS) on this effect of CRF and whether blockade of CRFR1 could prevent stress‐induced changes in the electrophysiological response, the animal’s behavior and in cell proliferation in the hippocampus. The behavior of the rats was monitored via a series of tests that formed part of the CUS. Electrophysiological measures of the BLA response to CRF, cell proliferation in the dentate gyrus and the expression of CRF and CRFR1 mRNA in amygdaloid nuclei were determinedex vivoafter completion of the CUS. CRF‐induced potentiation of afferent activation of the BLA was reduced in rats exposed to CUS, an effect that was inhibited by chronic antagonism of CRFR1. Furthermore, the reduction in BLA response to CRF was correlated with the anxiety trait of the animals, determined prior to initiation of the CUS. These results implicate CRFR1 in chronic stress‐induced alterations in amygdala function and behavior. Furthermore, they show that CRFR1 antagonists can prevent changes induced by chronic stress, in particular in those animals that are highly anxious.
Grueneberg ganglion neurons respond to cool ambient temperatures
Authors: Mamasuew Katharina , Breer Heinz , Fleischer Joerg
Published: November 2008

The Grueneberg ganglion (GG) – a neuronal cell cluster of unknown function localized to the vestibule of the anterior nasal cavity – is considered as a chemosensory compartment based on the expression of olfactory receptors and the olfactory marker protein. Axonal projection of GG neurons to so‐called ‘necklace glomeruli’ in the olfactory bulb of the brain, which are thought to be important for suckling behaviour in rodent pups, has led to the hypothesis that the GG might be involved in mother/child interactions. To survey potential activation of GG neurons in living animals during the course of mother/child interactions, expression of the activity‐dependent gene c‐Fos in the GG of neonatal mouse pups was monitored in the presence and absence of the dam. It was found that GG neurons were only activated in the absence of the mother. Moreover, GG activation was independent from olfactory cues as revealed by naris occlusion. Searching for stimuli eliciting GG activity in pups separated from the dam, cool ambient temperatures were found to induce strong c‐Fos expression in GG neurons whereas warmer temperatures did not. These coolness‐induced responses were only observed in a distinct subset of GG neurons characterized by the expression of the olfactory receptor V2r83. Finally, GG responsiveness to coolness was remarkably reduced in older stages. In summary, these findings suggest that the GG of neonatal mice is activated by cool ambient temperatures to which they are exposed in the absence of their dam, indicating that the GG might function as a thermosensor.
Acute and sensitized response to 3,4‐methylenedioxymethamphetamine in rats: different behavioral profiles reflected in different patterns of Fos expression
Authors: Colussi‐Mas Joyce , Schenk Susan
Published: November 2008

The behavioral profile in response to (±)‐3,4‐methylenedioxymethamphetamine (MDMA) is characterized by acute hyperlocomotion that is primarily restricted to the periphery of the open field, whereas behavioral sensitization to MDMA reflects a selective increase in activity in the central zone, suggesting that acute effects and sensitization might rely on neuroadaptations in different systems. This study was thus undertaken to determine whether specific changes in neuronal activation could be correlated with either the acute or sensitized behavioral responses to MDMA. Animals received five daily intraperitoneal (i.p.) injections of saline or MDMA (10 mg/kg). Two days later, animals that received saline were injected with saline or MDMA (5 or 10 mg/kg, i.p.). Animals pretreated with MDMA were injected with saline or MDMA (5 mg/kg, i.p.). Locomotor activity was measured in an open field, and neuronal activation was examined by immunodetection of Fos. Acute MDMA exposure produced a dose‐dependent increase in locomotion in the peripheral zone of the open field that was related to an increase in Fos expression in the ventromedial shell of the nucleus accumbens, ventral pallidum, several hypothalamic nuclei and rhomboid thalamic nucleus. Following repeated, intermittent exposure to MDMA, drug‐produced hyperactivity became sensitized but, unlike the effect of increasing dose, the increased response was due to increased activity and time spent in the central zone. Furthermore, the sensitized behavioral response was related to changes in Fos expression in the lateral shell of the nucleus accumbens, central nucleus of the amygdala and anteromedial part of the lateral habenula. This study identifies neural substrates that might specifically underlie the sensitized response to MDMA.
Conditioned effects of heroin on proinflammatory mediators require the basolateral amygdala
Authors: Szczytkowski Jennifer L. , Lysle Donald T.
Published: November 2008

Heroin administration alters the induction of nitric oxide, a molecule known to play a critical role in immune function. Previous research has shown that these alterations can be conditioned to environmental stimuli that have been associated with drug administration. Little is known about the brain areas that mediate these effects; however, the basolateral amygdala (BLA) has been implicated in the formation of stimulus–reward associations within models of drug abuse. The present study sought to determine whether inactivation of the BLA would alter heroin’s conditioned effects on the expression of inducible nitric oxide synthase (iNOS) and the proinflammatory cytokines TNF‐α and IL‐1β in the rat. The conditioning procedure involved repeated pairing of heroin with placement into a standard conditioning chamber. To test the conditioned response, animals were returned to the previously drug‐paired environment 6 days after the final conditioning session. Prior to testing, animals received intra‐BLA microinfusions of a mixture of the GABA agonists muscimol and baclofen. Following removal from the chambers on test day, all animals received subcutaneous lipopolysaccharide to induce systemic expression of iNOS, TNF‐α and IL‐1β. Analyses using real‐time RT‐PCR indicated that inactivation of the BLA blocked the suppressive effect of heroin‐associated environmental stimuli on iNOS induction and on the expression of the proinflammatory cytokines TNF‐α and IL‐1β in spleen and liver tissue. This study is important because it is the first to demonstrate that heroin’s conditioned effects on proinflammatory mediators require the BLA. These findings may have significant implications for the treatment of heroin users.
The type 1 cannabinoid receptor is highly expressed in embryonic cortical projection neurons and negatively regulates neurite growth in vitro
Authors: Vitalis Tania , Lainé Jeanne , Simon Anne , Roland Alexandre , Leterrier Christophe , Lenkei Zsolt
Published: November 2008

In the rodent and human embryonic brains, the cerebral cortex and hippocampus transiently express high levels of type 1 cannabinoid receptors (CB1Rs), at a developmental stage when these areas are composed mainly of glutamatergic neurons. However, the precise cellular and subcellular localization of CB1R expression as well as effects of CB1R modulation in this cell population remain largely unknown. We report that, starting from embryonic day 12.5, CB1Rs are strongly expressed in both reelin‐expressing Cajal‐Retzius cells and newly differentiated postmitotic glutamatergic neurons of the mouse telencephalon. CB1R protein is localized first to somato‐dendritic endosomes and at later developmental stages it localizes mostly to developing axons. In young axons, CB1Rs are localized both to the axolemma and to large, often multivesicular endosomes. Acute maternal injection of agonist CP‐55940 results in the relocation of receptors from axons to somato‐dendritic endosomes, indicating the functional competence of embryonic CB1Rs. The adult phenotype of CB1R expression is established around postnatal day 5. By using pharmacological and mutational modulation of CB1R activity in isolated cultured rat hippocampal neurons, we also show that basal activation of CB1R acts as a negative regulatory signal for dendritogenesis, dendritic and axonal outgrowth, and branching. Together, the overall negative regulatory role in neurite development suggests that embryonic CB1R signaling may participate in the correct establishment of neuronal connectivity and suggests a possible mechanism for the development of reported glutamatergic dysfunction in the offspring following maternal cannabis consumption.