Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid shift in substrate utilization driven by hypothalamic Agrp neurons

Agrp neurons drive feeding. To what extend these neurons participate in the regulation of other homeostatic processes is not well understood. We investigated the role of Agrp neurons in substrate utilization in mice. Activation of Agrp neurons was sufficient to rapidly increase RER and carbohydrate utilization, while decreasing fat utilization. These metabolic changes were linearly correlated with carbohydrates ingested, but not protein or fat ingestion. However, even in the absence of ingestive behaviors, activation of Agrp neurons led to changes in substrate utilization in well-fed mice. These effects were coupled to metabolic shifts towards lipogenesis. Inhibition of fatty acid synthetase (FAS) blunted the effects of Agrp neurons on substrate utilization. Finally, Agrp neurons controlled peripheral metabolism, but not food intake, via ß3-adrenergic receptor signaling in fat tissues. These results reveal a novel component of Agrp neuron-mediate metabolism regulation that involves sympathetic activity on fat compartments to shift metabolism towards lipogenesis.
Metabolite and Fatty Acid Analysis of Yeast Cells and Culture Supernatants

[Abstract] Metabolite and fatty acid analysis play important roles in evaluating the metabolic state of microorganisms. To examine the growth state and metabolism response of cells to environmental stress or genetic modification, intracellular and extracellular metabolites including fatty acids are usually analyzed to help understand the cellular biochemical changes in microorganisms. In this protocol, (gas chromatography-mass spectrometry based analysis was employed to investigate the fatty acids and other metabolites in yeast cells.
In vitro Regulatory T cells Differentiation From Naïve T Cells

[Abstract] In the past years, a subset of regulatory T cells (Tregs) expressing CD4, CD25 and the transcription factor FoxP3 has gained considerable attention as key regulators of T-cell tolerance and homeostasis (Sakaguchi, 2004). This population of T cells is specifically engaged in the maintenance of immune self-tolerance and the control of aberrant immune responses to foreign antigens. Remarkably, regulatory T cells have been implicated in tumor cell evasion of immune responses (Curiel et al., 2004; Zou, 2006) by suppressing T cell mediated antitumor immunity. The study of the signals that promote the differentiation of this suppressive population in the tumor microenvironment has become a central issue. Here we described a detailed method to in vitro differentiate Tregs using tumor cells conditioned media from mouse naïve T cells and to identify them based on their specifics markers (Dalotto-Moreno et al., 2013).
Biochemical aspects of nitrogen use efficiency: An overview

ABSTRACT Crop productivity relies heavily on nitrogen (N) fertilization. N is an essential macronutrient limiting the growth and development of plants in agriculture. Both organic and inorganic forms of N are metabolized in plants; nitrate and ammonia are common forms of inorganic N that can be metabolized in all plants. In the last 40 years the amount of synthetic N applied to crops has risen dramatically, resulting in significant increases in yield but with considerable impacts on the environment. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment. A requirement for crops that require decreased N fertilizer levels has been recognized in the call for a ‘Second Green Revolution’ and research in the field of nitrogen-use efficiency (NUE) has continued to grow. Nitrogen-use efficiency is inherently a complex trait, as each step-including N uptake, translocation, assimilation, and remobilization-is governed by multiple interacting genetic and environmental factors. The limiting factors in plant metabolism for maximizing NUE are different at high and low N supplies, indicating great potential for improving the NUE of present cultivars. Decreasing environmental losses and increasing the productivity of crop-acquired N requires the coordination of carbohydrate and N metabolism to give high yields. This has prompted a search to identify genes that improve the NUE of crop plants, with candidate NUE genes existing in pathways relating to N uptake, assimilation, amino acid biosynthesis, carbon (C)/N storage and metabolism, signaling and regulation of N metabolism and translocation, remobilization and senescence. In this review, we present the over view of N metabolism, relation of C/N metabolism and future prospects of improving NUE in crops using various complementary approaches.
Genetic variation in the Red-Listed moss Ditrichum cornubicum Paton (Ditrichaceae) and implications for its conservation

Ditrichum cornubicum is a rare and threatened acrocarpous moss found on copper-rich mine waste, characteristic of the EU protected habitat ‘Calaminarian grassland of the Violetalia calaminariae’. The species was once thought to be a British endemic, being known from two former copper/tin mine sites in Cornwall, until the discovery of a population in 2006 at Allihies Mountain Mine, Co. Cork, Ireland, a former copper mine. In light of this discovery, two theories of possible introduction from Britain to Ireland were put forward: (1) an introduction from the 1800s and (2) a more recent introduction (2000s). Only male plants of the species are known, and reproduction and dispersal are therefore solely through asexual propagules and fragmentation. In order to address the conservation questions of the origin of the Irish population and to determine whether diversity exists within this rare species, genetic fingerprinting (amplified fragment length polymorphism) was carried out on the three known global populations. Percent polymorphism was found to be 7.29% and Nei's total gene diversity (HT) was 0.0356. AMOVA revealed that, of the small amount of variation found, the majority was among the three populations (98%). The presence of five private alleles in the Allihies population suggests a longer period of isolation than would fit either theory of introduction. Cluster analyses reveal that the Allihies population is more genetically distinct than the two British populations are to each other, thus heightening the conservation priority for this population.
Effects of duration of preservation and glycerol percentages on quality of frozen ram semen

The aims of the present study were to determine the effectiveness of the undertaken freezing technique of indigenous ram semen (with different percentages of glycerol and different thawing times) by observing the post thaw motility at 24, 48 and 72 hours of preservation. Nine ejaculates were collected from each 6 mature rams using artificial vagina method. The ejaculates were frozen using Tris-citric acid egg yolk media having different percentages of glycerol (3, 5, and 7) in two step dilution method. The post thaw motility was observed in different temperature (37 0 , 40 0 and 45 0 C) and time (12, 12 and 10 seconds). The motility percentages after freezing for 24, 48 and 72 hours of duration varied from 8-50%, 8-50% and 445%. The significantly highest (P<0.01) motility (35.3 ± 7.8%) was observed after 24 hours of preservation compared with 48 and 72 hours (30.6 ± 8.0%, 28.8 ± 7.9%). The normal morphology percentages after freezing of ram semen for 24, 48 and 72 hours of duration varied from 63-89%, 60-85%, and 58-80%. The significantly highest (P<0.05) normal morphology (79.9 ± 4.0%) was observed after 24 hours of preservation compared with 48 and 72 hours (75.8 ± 4.4%, 73.3 ± 4.6%). The significantly highest (P<0.01) sperm motility (39.1 ± 5.8%) was observed with 5% glycerol, at 40 0 C for 12 seconds thawing temperature and time compared with 37 0 C for 12 seconds and 45 0 C for 10 seconds, respectively. The study revealed a preliminary data which deserve further study to optimize the measures for sustainable freezing of indigenous ram semen.
Comparative breeding biology of the two bill morphs of the black-bellied seedcracker

Comparaison de la biologie de la reproduction pour les 2 formes de bec existantes au sein d'une meme population de Pyrenestes ostrinus, au Cameroun. Tentative de mise en evidence de divergences temporelles ou spatiales indicatives d'un processus de speciation telles que choix du site de nidification, timing de la nidification en relation avec les pluies et les ressources alimentaires, influence du comportement ou de la predation
Tick Infestations and Their Consequences for Migratory Songbirds During Spring Stopover

TICK INFESTATIONS AND THEIR CONSEQUENCES FOR MIGRATORY SONGBIRDS DURING SPRING STOPOVER by Johnny Michael Sellers, Jr. December 2011 Migratory birds face a number of challenges during their seasonal movement from tropical/sub-tropical Central and South America to more temperate North America. Maintaining health during migration is of particular concern. This study seeks to understand how haematophageous ectoparasites, such as ticks (Ixodida), impact host body condition as they feed on passerines during migration. We hypothesized that foraging location would impact tick acquisition by migrants and that tick burdens during migration would negatively impact body condition. We surveyed 2,064 birds during spring 2009 and 2010 and found that 2.4% of the surveyed birds were infested with one or more ticks (23 avian species). Ticks are more abundant in low vegetation and on the ground, but species-specific foraging niche did not predict the likelihood of obtaining ticks among migratory birds. Furthermore, birds without ticks were no more likely to be in better body condition than birds with ticks, though body condition tended to decrease with tick burden. Additionally, avian blood and feeding ticks were collected and analyzed via PCR for the presence of Ehrlichia chaffeensis, causative agent of the tickborne disease ehrlichiosis, to determine if ticks and their associated pathogens are capable of being transported to North America by way of migrating birds. We found that 27 (10.2%) of252 blood samples were positive for E. chaffeensis and 109 (97.3%) of the 112 collected ticks were not native to North America.
Niche partitioning by three Pterodroma petrel species during non-breeding in the equatorial Pacific Ocean

Niche divergence is expected for species that compete for shared resources, including migrants that occupy similar regions during the non-breeding season. Studies of temperate seabirds indicate that both spatial and behavioural segregation can be important mechanisms for reducing competition, but there have been few investigations of resource partitioning by closely related taxa in low productivity, tropical environments. We investigated niche partitioning in 3 gadfly petrel taxa, Pterodroma leucoptera leucoptera (n = 22), P. leucoptera caledonica (n = 7) and P. pycrofti (n = 12), during their non-breeding season in the eastern tropical Pacific Ocean by combining tracking data from geolocator-immersion loggers with remotely sensed environmental data in species distribution models (SDMs), and by comparing feather stable isotope ratios. The 3 taxa showed spatial partitioning: two foraged in the North Equatorial Counter Current and one in the South Equatorial Current. This reflected differences in their realised habitat niches, with significant taxon-specific responses to thermocline depth, sea surface temperature and bathymetry. There were also differences among taxa in activity patterns, and all birds spent a much larger proportion of time in flight at night than during the day, suggesting predominance of nocturnal foraging behaviour. Comparison of stable isotope ratios in feathers suggests that P. l. leucoptera and P. pycrofti mainly consume vertically migrating mesopelagic fishes, whereas the diet of P. l. caledonica also includes some lower trophic levels including crustaceans and squid. Unique insights can be gained from studies of the foraging ecology of tropical pelagic seabirds, in comparison with temperate and polar waters, and are urgently required for understanding and protecting tropical avifauna in key marine habitats.
Soil quality indicators to assess functionality of restored soils in degraded semiarid ecosystems

A thorough knowledge of soil functionality is critical to successful restoration of disturbed ecosystems, and its evaluation involves the assessment of soil properties and processes as a component of a healthy ecosystem. Here, we propose a set of soil quality indicators to assess the soil status in restored soils (topsoil and waste material) and test new methods that are easy to apply, interpret, and cost‐effective for the analysis of soil biological indicators in restored ecosystems. We show that in addition to organic carbon and C:N ratio, biological indicators (microbial diversity and activity in particular) are the most sensitive indicators to detect differences among reconstructed soils and analogue undisturbed soils in semiarid areas. The use of the 1‐day CO2 test is proven to be an alternative cost‐ and time‐effective method to measure microbial activity and assess soil functionality of restored soils. Our results show a positive effect of vegetation on reconstructed soils and a recovery of soil functionality in waste material to levels similar to topsoil once vegetation is established. However, soil functionality in both restored waste materials and topsoils is still far from that in undisturbed native soils. We conclude that soil functionality is critical in the restoration process, particularly in semiarid areas, and the methods used here could be effectively applied in a broad range of restoration projects in arid and semiarid environments.
Epicuticular Wax Morphology and Composition are Related to Grapefruit Chilling Injury

Differences in chilling injury (CI) susceptibitity between 'Marsh' grapefruit (Citrus paradisi Macf.) from interior and exterior tree canopy positions were analyzed to investigate the hypothesis that epicuticular wax morphology and composition influence CI development during low-temperature storage. The sun-exposed surface of fruit from the exterior canopy had significantly more CI and larger wax platelets than the shaded surface of the same fruit. Interior canopy fruit had significantly less CI and smaller wax platelets than exterior canopy fruit. Hydrocarbons, primarily n-alkanes, were significantly more abundant in the epicuticular wax on the surfaces of sun-exposed and exterior fruit compared with surfaces of shaded and interior fruit, respectively [. ]
Banco de sementes do solo após aplicação de herbicidas pré-emergentes durante quatro safras de cana-de-açúcar

The objective of this work was to evaluate the effect of the pre-emergent herbicides indaziflam, indaziflam+metribuzin, and diuron+hexazinone on the soil seed bank of a sugarcane crop, during four consecutive harvests. The experimental design was a randomized complete block with four replicates in a split plot. Treatments consisted of doses of the following herbicides: indaziflam, 75, 100, and 150 g a.i. ha -1 ; indaziflam+metribuzin, 75 + 960 g a.i. ha -1 ; and diuron+hexazinone, 936 + 264 g a.i. ha -1 ; besides a clean area, used as a reference. The soil seed bank was analyzed in the 0.00‒0.10 and 0.10‒0.20-m soil layers. Emerged seedlings were counted and identified, and absolute and relative density, frequency and abundance, as well as the importance value index, were calculated. In the treatments 100 and 150 g a.i. ha -1 indaziflam, there was a greater reduction in the total seed bank and in the importance value index of species of Poaceae and Asteraceae. The total seed bank, in the 0.10‒0.20-m layer, and that of the species Portulaca oleracea , in both evaluated layers, are not affected by the herbicides. The use of pre-emergent herbicides during four consecutive harvests decreases the soil seed bank in the 0.00‒0.10-m layer under a sugarcane crop.
Effect of mesenchymal stem cells on movement and urination of rats with spinal cord injury.

A terapia celular tem sido reportada como possibilidade de tratamento para os traumas medulares, frequentes em pessoas e em animais, e que nao apresentam cura farmacologica para danos advindos da lesao primaria. Foram avaliados os efeitos da aplicacao de celulas-tronco derivadas do tecido adiposo humano (hADSC) em ratos Wistar apos lesao medular. As hADSC foram cultivadas, utilizadas entre a terceira e quinta passagens e parte delas foi transduzida para o rastreamento in vivo apos o transplante. A lesao medular foi realizada com cateter de Fogarty no. 3, introduzido no espaco epidural, com cuff localizado em T8 e preenchido com 80 ? L de solucao salina, por 5 minutos. Os animais do grupo controle (A, n=12) receberam aplicacoes de meio de cultura (50 ? L) e o grupo B (n=12) recebeu duas aplicacoes de hADSC (1,2 x 106), sete e 14 dias pos-lesao, ambas na veia da cauda. O esvaziamento vesical, por massagem, foi efetuado diariamente, durante tres meses. As avaliacoes motoras foram repetidas, diariamente, ate tres meses pos-lesao, utilizando a escala Basso-Beattie-Bresneham. Apos este periodo os animais foram submetidos a eutanasia e foram realizadas analises histologicas de bexiga urinaria e medula espinhal. As analises de bioluminescencia revelaram hADSC no local da aplicacao e nos pulmoes. Houve melhora da funcao da bexiga urinaria em 83,3% dos animais do grupo B e 16,66% dos animais do grupo A. A analise das avaliacoes motoras e histologicas das medulas espinhais e bexigas urinarias nao demonstrou diferencas significativas entre os grupos A e B. Os resultados indicam que as hADSC transplantadas influenciaram a miccao, de forma benefica, por um mecanismo de acao a distância, telecrino.
INFLUENCE OF DIET ON POPULATION GROWTH AND ALLERGEN PRODUCTION IN CULTURED HOUSE DUST MITES - DERMATOPHAGOIDES FARINAE AND DERMATOPHAGOIDES PTERONYSSINUS

Poola, Swetha Avula. M.S., Department of Biological Sciences, Wright State University, 2009. Influence of Diet on Population Growth and Allergen Production in Cultured House Dust Mites Dermatophagoides farinae and Dermatophagoides pteronyssinus. Dermatophagoides farinae and Dermatophagoides pteronyssinus culture extracts are used for skin testing, immunotherapy and research studies. There is a need to develop an effective culture method so that standardized extracts and allergens can be produced. The purpose of this study was to examine if different diets effect mite population growth and the amount of allergen produced in cultures. Dermatophagoides farinae and Dermatophagoides pteronyssinus were cultured on diets A and B. The density of mites, life stage composition and allergen concentration was determined at two week intervals. Enzyme-linked immune sorbent assays (ELISA) were used to assess group 1 and group 2 allergen concentrations. This study showed that diet is an important factor for culturing of mites. Diet B was found to be better suited to culture Dermatophagoides farinae whereas diet A was better for culturing of Dermatophagoides pteronyssinus. Diet A cultures of Dermatophagoides pteronyssinus produced greater concentrations of group 2 allergen than diet B.
The Study of Histopathological Changes upon Exposure to Vinegerized Copper Sulphate in Liver and Kidney of Broiler Chick

Copper sulfate is used as a fungicide in poultry feed and for the medication of drinking water. Sub acute copper poisoning is rare but chronic copper poisoning is frequently observed. Ninety chicks were used for the present study and they were divided into five groups (A, B, C, D and E) on the basis of various treatment schedule of vinegarized copper sulfate in feed (100mg, 500mg, 1gm and 2gm). At the end of each week weight gain, feed consumption, morphology and histopathology of liver and kidney were noted. Chicks showed various clinical symptoms including loose fecal material, poor feather growth, entheritus and coccidosis disease. Major histopathological changes were degeneration of cells, infiltration of mononuclear cells and necrosis. The type and extent of lesions varied with the duration and age of chicks.
Monovalent Cation Doping of CH$_{3}$NH$_{3}$PbI$_{3}$ for Efficient Perovskite Solar Cells

M. Abdi-Jalebi thanks Nava Technology Limited for a PhD scholarship. M.I. Dar and M. Gratzel thank the King Abdulaziz City for Science and Technology (KACST) and Swiss National Science Foundation (SNSF) for financial support. The authors would like to thank Dr. Pierre Mettraux in Molecular and Hybrid Materials Characterization Center, EPFL for carrying out XPS measurements. A. Sadhanala gratefully acknowledges financial support from the Indo-UK APEX project. S.P. Senanayak acknowledges Royal Society London for the Newton Fellowship. R.H. Friend, M. Abdi-Jalebi, and A. Sadhanala would like to acknowledge the support from EPSRC.
Circadian clock, cell cycle, and breast cancer: an updated review

Abstract Some key elements are common to two fundamental periodic regulatory processes; the circadian cycle and the cell cycle. Underlying mechanisms of coordination between the two processes are critical for proper cellular functioning and physiology. Disruption in the mechanisms of one process may affect the role of other that may direct critical physiological changes and may cause severe diseases like cancer, etc. More or less persuasive evidences evolve from the breast cancer research. In this mini review, we highlighted the molecular coordination’s of the elements of circadian cycle and the cell cycle and their altered expressions associated with the genesis and progression of breast cancer.
Establishment of a new method for isolation and culture of equine endometrial epithelial and stromal cells.

In general, in vitro culture is an appropriate model to investigate the physiology, interaction and differentiation of different cell types under controlled and defined conditions (Freshney 1990), for the better understanding of the pathogenesis and the etiology of several diseases (Findlay et al. 1990). Because preliminary tests could be accomplished using this technique one can reduce the number of animal experiments, as well.
Induced Abscission Sites in Internodal Explants of Impatiens sultani: A New System for Studying Positional Control with an Appendix: A Mathematical Model for Abscission Sites

Intemodes from Impatiens sultani shoots, explanted into sterile culture, often developed a transverse separation layer after one to two weeks and the top then abscised from the bottom of the explant. Such abscission occurred more rapidly and in a greater proportion of explants when 00001 per cent auxin (IAA) was provided basally and when younger intemodes and shorter explants were used. The distance of the separation layer from the base of the explant varied little with explant length, but increased with the concentration of auxin applied basally. It seems that in this adventitious abscission the processes of positional definition and differentiation proceed without pause, whereas in normal abscission the position is defined early in development but the final stage of differentiation of the separation layer is delayed until much later when the organ senesces. To account for the results from the internodal explants and from surgical operations on shoots as well as for the characteristic position of abscission sites of leaves and fruits, we suggest that the position of abscission is controlled primarily by auxin acting as a morphogen: abscission sites occur at Y-junctions just above the base of the arm with the lower activity and auxin status, or in single axes above a region of higher auxin status. In both sites, the auxin concentration decreases in the apical direction. This hypothesis is supported by a mathematical model (see Appendix) of the interaction of diffusive and polar transport in controlling the concentration gradient along intemodes with specified auxin concentrations maintained basally. The model allows predictions concerning the site and timing of abscission which accord with observations on intemodal explants.