bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies Peroxisome Proliferator-Activated Receptor Gammaas an intrinsic negative regulator of viral replication
Authors: Bernier Annie , Cleret-Buhot Aurélie , Zhang Yuwei , Goulet Jean-Philippe , Monteiro Patricia , Gosselin Annie , DaFonseca Sandrina , Wacleche Vanessa Sue , Jenabian Mohammad-Ali , Routy Jean-Pierre , Tremblay Cécile , Ancuta Petronela 
Published: December 2013

AbstractBackgroundWe previously demonstrated that primary Th1Th17 cells are highly permissive to HIV-1, whereas Th1 cells are relatively resistant. Molecular mechanisms underlying these differences remain unknown.ResultsExposure to replication competent and single-round VSV-G pseudotyped HIV strains provide evidence that superior HIV replication in Th1Th17vs.Th1 cells was regulated by mechanisms located at entry and post-entry levels. Genome-wide transcriptional profiling identified transcripts upregulated (n = 264) and downregulated (n = 235) in Th1Th17vs.Th1 cells (p-value < 0.05; fold change cut-off 1.3).Gene Set Enrichment Analysisrevealed pathways enriched in Th1Th17 (nuclear receptors, trafficking, p38/MAPK, NF-κB, p53/Ras, IL-23)vs.Th1 cells (proteasome, interferon α/β). Differentially expressed genes were classified into biological categories usingGene Ontology. Th1Th17 cells expressed typical Th17 markers (IL-17A/F, IL-22, CCL20, RORC, IL-26, IL-23R, CCR6) and transcripts functionally linked to regulating cell trafficking (CEACAM1, MCAM), activation (CD28, CD40LG, TNFSF13B, TNFSF25, PTPN13, MAP3K4, LTB, CTSH), transcription (PPARγ, RUNX1, ATF5, ARNTL), apoptosis (FASLG), and HIV infection (CXCR6, FURIN). Differential expression of CXCR6, PPARγ, ARNTL, PTPN13, MAP3K4, CTSH, SERPINB6, PTK2, and ISG20 was validated by RT-PCR, flow cytometry and/or confocal microscopy. The nuclear receptor PPARγ was preferentially expressed by Th1Th17 cells. PPARγ RNA interference significantly increased HIV replication at levels post-entry and prior HIV-DNA integration. Finally, the activation of PPARγ pathwayviathe agonist Rosiglitazone induced the nuclear translocation of PPARγ and a robust inhibition of viral replication.ConclusionsThus, transcriptional profiling in Th1Th17vs. Th1 cells demonstrated that HIV permissiveness is associated with a superior state of cellular activation and limited antiviral properties and identified PPARγ as an intrinsic negative regulator of viral replication. Therefore, triggering PPARγ pathwayvianon-toxic agonists may contribute to limiting covert HIV replication and disease progression during antiretroviral treatment.
Activation of Cyclin-Dependent Kinase 5 Mediates Orofacial Mechanical Hyperalgesia
Authors: Prochazkova Michaela , Terse Anita , Amin Niranjana D , Hall Bradford , Utreras Elias , Pant Harish C , Kulkami Ashok B 
Published: December 2013

Background Cyclin-dependent kinase 5 (Cdk5) is a unique member of the serine/threonine kinase family. This kinase plays an important role in neuronal development, and deregulation of its activity leads to neurodegenerative disorders. Cdk5 also serves an important function in the regulation of nociceptive signaling. Our previous studies revealed that the expression of Cdk5 and its activator, p35, is upregulated in nociceptive neurons during peripheral inflammation. The aim of the present study was to characterize the involvement of Cdk5 in orofacial pain. Since mechanical hyperalgesia is the distinctive sign of many orofacial pain conditions, we adapted an existing orofacial stimulation test to assess the behavioral responses to mechanical stimulation in the trigeminal region of the transgenic mice with either reduced or increased Cdk5 activity. Results Mice overexpressing or lacking p35, an activator of Cdk5, showed altered phenotype in response to noxious mechanical stimulation in the trigeminal area. Mice with increased Cdk5 activity displayed aversive behavior to mechanical stimulation as indicated by a significant decrease in reward licking events and licking time. The number of reward licking/facial contact events was significantly decreased in these mice as the mechanical intensity increased. By contrast, mice deficient in Cdk5 activity displayed mechanical hypoalgesia. Conclusions Collectively, our findings demonstrate for the first time the important role of Cdk5 in orofacial mechanical nociception. Modulation of Cdk5 activity in primary sensory neurons makes it an attractive potential target for the development of novel analgesics that could be used to treat multiple orofacial pain conditions.
Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling
Authors: Oakey Helena , Shafiei Reza , Comadran Jordi , Uzrek Nicola , Cullis Brian , Gomez Leonardo D , Whitehead Caragh , McQueen-Mason Simon J , Waugh Robbie , Halpin Claire 
Published: December 2013

Abstract

Background
In this study, a multi-parent population of barley cultivars was grown in the field for two consecutive years and then straw saccharification (sugar release by enzymes) was subsequently analysed in the laboratory to identify the cultivars with the highest consistent sugar yield. This experiment was used to assess the benefit of accounting for both the multi-phase and multi-environment aspects of large-scale phenotyping experiments with field-grown germplasm through sound statistical design and analysis.

Results
Complementary designs at both the field and laboratory phases of the experiment ensured that non-genetic sources of variation could be separated from the genetic variation of cultivars, which was the main target of the study. The field phase included biological replication and plot randomisation. The laboratory phase employed re-randomisation and technical replication of samples within a batch, with a subset of cultivars chosen as duplicates that were randomly allocated across batches. The resulting data was analysed using a linear mixed model that incorporated field and laboratory variation and a cultivar by trial interaction, and ensured that the cultivar means were more accurately represented than if the non-genetic variation was ignored. The heritability detected was more than doubled in each year of the trial by accounting for the non-genetic variation in the analysis, clearly showing the benefit of this design and approach.

Conclusions
The importance of accounting for both field and laboratory variation, as well as the cultivar by trial interaction, by fitting a single statistical model (multi-environment trial, MET, model), was evidenced by the changes in list of the top 40 cultivars showing the highest sugar yields. Failure to account for this interaction resulted in only eight cultivars that were consistently in the top 40 in different years. The correspondence between the rankings of cultivars was much higher at 25 in the MET model. This approach is suited to any multi-phase and multi-environment population-based genetic experiment.
Membranous nephropathy with acquired factor V inhibitor: a case report
Authors: Kitamura Shinji , Misawa Mahito , Namba Sayaka , Tsuji Kenji , Torigoe Rikako , Shima Midori , Makino Hirofumi 
Published: December 2013

Abstract

Background
Membranous nephropathy is one of the most common causes of nephrotic syndrome in adults. In contrast, acquired factor V inhibitor is a rare bleeding disorder.

Case presentation
A 62-year-old Asian man with a history of cerebral hemorrhage, purpura, eosinophilia and hyper immunoglobulin E syndrome developed proteinuria. The bleeding disorder was diagnosed with acquired factor V inhibitors. A renal biopsy revealed that he suffered from membranous nephropathy with glomerular endothelial damage which is reported to be involved in another factor disorder. After the steroid administration, the coagulation test and proteinuria were improved.

Conclusions
The presence of factor V inhibitors may have been involved in the development of membranous nephropathy.
Dual potential of microalgae as a sustainable biofuel feedstock and animal feed
Authors: Lum Krystal K , Kim Jonggun , Lei Xin Gen 
Published: December 2013

AbstractThe rise in global population has led to explorations of alternative sources of energy and food. Because corn and soybean are staple food crops for humans, their common use as the main source of dietary energy and protein for food-producing animals directly competes with their allocation for human consumption. Alternatively, de-fatted marine microalgal biomass generated from the potential biofuel production may be a viable replacement of corn and soybean meal due to their high levels of protein, relatively well-balanced amino acid profiles, and rich contents of minerals and vitamins, along with unique bioactive compounds. Although the full-fatted (intact) microalgae represent the main source of omega-3 (n-3) polyunsaturated fatty acids including docohexaenoic acid (DHA) and eicosapentaenoic acid (EPA), the de-fatted microalgal biomass may still contain good amounts of these components for enriching DHA/EPA in eggs, meats, and milk. This review is written to highlight the necessity and potential of using the de-fatted microalgal biomass as a new generation of animal feed in helping address the global energy, food, and environmental issues. Nutritional feasibility and limitation of the biomass as the new feed ingredient for simple-stomached species are elaborated. Potential applications of the biomass for generating value-added animal products are also explored.
Temperature during embryonic development has persistent effects on metabolic enzymes in the muscle of zebrafish
Authors: Schnurr Meghan E. , Yin Yi , Scott Graham R. 
Published: December 2013

SummaryGlobal warming is intensifying interest in the physiological consequences of temperature change in ectotherms, but we still have a relatively poor understanding of the effects of temperature on early life stages. This study determined how embryonic temperature (TE) affects development and the activity of metabolic enzymes in the swimming muscle of zebrafish. Embryos developed successfully to hatching (survival ≥ 88%) from 22°C to 32°C, but suffered sharp increases in mortality outside of this range. Embryos that were incubated until hatching at a control TE (27°C) or near the extremes for successful development (22°C or 32°C) were next raised to adulthood under control conditions at 27°C. Growth trajectories after hatching were altered in the 22°C and 32°C TE groups compared to 27°C TE controls, but growth slowed after 3 months of age in all groups. Maximal enzyme activities of cytochrome c oxidase (COX), citrate synthase (CS), hydroxyacyl-coA dehydrogenase (HOAD), pyruvate kinase (PK), and lactate dehydrogenase (LDH) were measured across a range of assay temperatures (22°C, 27°C, 32°C, 36°C) in adults from each TE group that were acclimated to 27°C or 32°C. Substrate affinities (Km) were also determined for COX and LDH. In adult fish acclimated to 27°C, COX and PK activities were higher in 22°C and 32°C TE groups than in 27°C TE controls, and the temperature optimum for COX activity was higher in the 32°C TE group than in the 22°C TE group. Warm acclimation reduced COX, CS, and/or PK activities in the 22°C and 32°C TE groups, possibly to compensate for thermal effects on molecular activity. This response did not occur in the 27°C TE controls, which instead increased LDH and HOAD activities. Warm acclimation also increased thermal sensitivity (Q10) of HOAD to cool temperatures across all TE groups. We conclude that the temperature experienced during early development can have a persistent impact on energy metabolism pathways and acclimation capacity in later life.
Blood feeding induces hemocyte proliferation and activation in the African malaria mosquito, Anopheles gambiae Giles
Authors: Bryant William B. , Michel Kristin 
Published: December 2013

Summary
Malaria is a global public health problem especially in sub-Saharan Africa, where the mosquito Anopheles gambiae Giles serves as the major vector for the protozoan Plasmodium falciparum Welch. One determinant of malaria vector competence is the mosquito's immune system. Hemocytes are a critical component as they produce soluble immune factors that either support or prevent malaria parasite development. However, despite their importance in vector competence, understanding of their basic biology is just developing. Applying novel technologies to the study of mosquito hemocytes, we investigated the effect of blood meal on hemocyte population dynamics, DNA replication, and cell cycle progression. In contrast to prevailing published work, data presented here demonstrate that hemocytes in adult mosquitoes continue to undergo low basal levels of replication. In addition, blood ingestion caused significant changes in hemocytes with 24 h. Hemocytes displayed an increase in cell number, size, granularity, and Ras-MAPK signaling as well as altered cell surface moieties. As these changes are well-known markers of immune cell activation in mammals and Drosophila melanogaster Meig., we further investigated if a blood meal changes the expression of hemocyte-derived immune factors. Indeed, hemocytes 24 h post blood meal displayed higher levels of critical components of the complement and melanization immune reactions in mosquitoes. Taken together, this study demonstrates that the normal physiological process of a blood meal activates the innate immune response in mosquitoes. This process is likely in part regulated by Ras-MAPK signaling, highlighting a novel mechanistic link between blood feeding and immunity.
Urea-based osmoregulation in the developing embryo of oviparous cartilaginous fish (Callorhinchus milii): contribution of the extraembryonic yolk sac during the early developmental period
Authors: Takagi Wataru , Kajimura Makiko , Tanaka Hironori , Hasegawa Kumi , Bell Justin D. , Toop Tes , Donald John A. , Hyodo Susumu 
Published: December 2013

SummaryMarine cartilaginous fish retain a high concentration of urea to maintain the plasma slightly hyperosmotic to the surrounding seawater. In adult fish, urea is produced by hepatic and extrahepatic ornithine urea cycles (OUCs). However, little is known about the urea retention mechanism in developing cartilaginous fish embryos. In order to address the question as to the mechanism of urea-based osmoregulation in developing embryos, the present study examined the gene expression profiles of OUC enzymes in oviparous holocephalan elephant fish (Callorhinchus milii) embryos. We found that the yolk sac membrane (YSM) makes an important contribution to the ureosmotic strategy of the early embryonic period. The expression of OUC enzyme genes was detectable in the embryonic body from at least stage 28, and increased markedly during development to hatching, which is most probably due to growth of the liver. During the early developmental period, however, the expression of OUC enzyme genes was not prominent in the embryonic body. Meanwhile, we found that the mRNA expression of OUC enzymes was detected in extraembryonic YSM; the mRNA expression of cmcpsIII in the YSM was much higher than that in the embryonic body during stages 28-31. Significant levels of enzyme activity and the existence of mitochondrial-type cmgs1 transcripts in YSM supported the mRNA findings. We also found that the cmcpsIII transcript is localized in the vascularized inner layer of the YSM. Taken together, our findings demonstrate for the first time that the YSM is involved in urea-based osmoregulation during the early to mid phase of development in oviparous cartilaginous fish.
Role of axial muscles in powering mouth expansion during suction feeding in Largemouth Bass
Authors: Camp Ariel , Brainerd Elizabeth 
Published: December 2013

SummarySuction-feeding fishes capture food by fast and forceful expansion of the mouth cavity, and axial muscles likely provide substantial power for this feeding behavior. Dorsal expansion of the mouth cavity can only be powered by the epaxial muscles, but both the sternohyoid, shortening against an immobile pectoral girdle to retract the hyoid, or the hypaxial muscles, shortening to retract both the pectoral girdle and hyoid, could contribute ventral expansion power. To determine 1) if hypaxial muscles generate power for ventral expansion, and 2) the rostrocaudal extent of axial muscle shortening during suction feeding, we measured skeletal kinematics and muscle shortening in largemouth bass (Micropterus salmoides). The 3D motions of the cleithrum and hyoid were measured with X-ray Reconstruction of Moving Morphology (XROMM), and muscle shortening was measured with fluoromicrometry, wherein changes in the distance between radio-opaque intramuscular markers are measured with biplanar x-ray video. We found that the hypaxials generated power for ventral suction expansion, shortening (mean of 6.2 mm) to rotate the pectoral girdle caudoventrally (mean of 9.3°) and retract the hyoid (mean of 8.5 mm). In contrast, the sternohyoid shortened minimally (mean of 0.48 mm), functioning like a ligament to transmit hypaxial shortening to the hyoid. Hypaxial and epaxial shortening were not confined to the rostral muscle regions, but extended more than halfway down the body during suction expansion. We conclude that hypaxial and epaxial muscles are both crucial for powering mouth expansion in largemouth bass, supporting the integration of axial and cranial musculoskeletal systems for suction feeding.
Special K: testing the potassium link between radioactive rubidium (86Rb) turnover and metabolic rate
Authors: Tomlinson Sean , Mathialagan Priya D. , Maloney Shane K. 
Published: December 2013

Summary
The measurement of 86Rb turnover recently has been suggested as a useful method of measuring field metabolic rate in small animals. We investigated a proposed mechanism of 86Rb turnover, its analogy for K+, by comparing the turnover of 86Rb in a model insect, the rhinoceros beetle Xylotrupes gideon, fed diets of plum jam, or plum jam enriched with K+ or Rb+. The turnover of 86Rb in the beetles on the K+ and the Rb+ diets was higher than on the Jam diet (F2, 311 = 32.4; p = 1.58 × 10-13). We also exposed the beetles to different ambient temperatures to induce differences in metabolic rate (VCO2) while feeding them the Jam and K+ diets. VCO2 was higher at higher Ta for both Jam (F1,11 = 14.56; p = 0.003) and K+ (F1,8 = 15.39; p = 0.004) dietary groups, and the turnover of 86Rb was higher at higher Ta for both Jam (F1,11 = 10.80; p = 0.007) and K+ (F1,8 = 12.34; p = 0.008) dietary groups. There was a significant relationship between 86Rb turnover and VCO2 for both the Jam (F1,11 = 35.00; p = 1.0× 10-3) and the K+ (F1,8 = 64.33; p = 4.3 × 10-5) diets, but the relationship differed between the diets (F1,19 = 14.07; p = 0.001), with a higher 86Rb turnover on the K+-enriched than the Jam diet at all Ta. We conclude that 86Rb turnover is related to K+ metabolism, and that this is the mechanism of the relationship between 86Rb turnover and VCO2. Studies relating the 86Rb turnover to VCO2 should maintain dietary [K+] as close as possible to natural diets for the most accurate calibrations for free-ranging animals.
Differential effects of specific carotenoids on oxidative damage and immune response of gull chicks
Authors: Lucas Alberto , Morales Judith , Velando Alberto 
Published: December 2013

Summary
Micronutrients are essential for normal metabolic processes during early development. Concretely, it has been suggested that diet-derived carotenoids can play a key role in physiological functions due to their antioxidant and immunostimulant properties. However, their role as antioxidants remains controversial. Additionally, it is also unclear whether oxidative stress mediates their immunostimulatory effects. In this field study, we separately supplemented yellow-legged gull (Larus michahellis, Naumann 1840) chicks with two carotenoids (lutein and β-carotene) with different molecular structure and different transformation pathways into other oxidative forms of carotenoids. We quantified their effect on the oxidative status and the immune response of chicks before and after an oxidative challenge with Paraquat, a pro-oxidant molecule. Prior to oxidative challenge, no carotenoid treatment affected the oxidative status of chicks, but they enhanced the inflammatory response to an antigen compared to controls. The oxidative challenge enhanced plasma vitamin E levels (but not in β-carotene supplemented chicks) and the antioxidant capacity in the short term. Interestingly, lutein-supplemented chicks showed lower oxidative damage to proteins than non-lutein supplemented chicks. After the oxidative challenge, the positive effect of carotenoid supplementation on the immune response disappeared. Thus, these results suggest differential effects of two carotenoids with different molecular structure on the oxidative status. Lutein but not β-carotene helps to combat oxidative damage after a free-radical exposure. Additionally, the results indicate that the immunostimulatory effects of carotenoids are linked to oxidative status during early life.
The smell of moulting:N-acetylglucosamino-1,5-lactone is a premoult biomarker and candidate component of the courtship pheromone in the urine of the blue crab,Callinectes sapidus
Authors: Kamio Michiya , Schmidt Manfred , Germann Markus W. , Kubanek Julia , Derby Charles D. 
Published: December 2013

SummaryFemale blue crabs (Callinectes sapidus) in their pubertal moult stage release unidentified sex pheromone molecules in their urine, causing males to respond with courtship behaviours including a display called courtship stationary paddling and a form of precopulatory guarding called cradle carry. We hypothesized that pheromones are mixtures of molecules and are more concentrated in urine of pubertal premoult females compared to other moulting stages and thus that these molecules are biomarkers (i.e. metabolites that can be used as an indicator of some biological state or condition) of pubertal premoult females. We tested this hypothesis by combining bioassay-guided fractionation and biomarker targeting. To evaluate the molecular mass of the putative pheromone by bioassay-guided fractionation, we separated urine from pubertal premoult females and intermoult males by ultrafiltration into three molecular mass fractions. The &lt;500 Da fraction and the 500-1000 Da fraction but not the &gt;1000 Da fraction of female urine induced male courtship stationary paddling, but none of the fractions of male urine did. Thus, female urine contains molecules &lt;1000 Da that stimulate courtship behaviours in males. Biomarker targeting using NMR spectral analysis of the 500-1000 Da fraction of urine from premoult and postmoult males and females revealed a premoult biomarker. Purification, NMR, mass spectrometry, and HPLC analysis of this premoult biomarker identified it as N-acetylglucosamino-1,5-lactone (NAGL) and showed that it is more abundant in urine of premoult females and males than in urine of either postmoult or juvenile females and males. NAGL has not been reported before as a natural product or as a molecule of the chitin metabolic pathway. Physiological and behavioural experiments demonstrated that blue crabs can detect NAGL through their olfactory pathway. Thus, we hypothesize that NAGL is a component of the sex pheromone and that it acts in conjunction with other yet unidentified components.