Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and fine mapping of a potassium dependent growth QTL in Arabidopsis

Potassium is an essential macronutrient for plants. Deficiency in potassium leads to a reduction in organ growth and can cause yield loss. Previously, a quantitative trait locus (QTL) analysis was performed with a Ler/Kas-2 recombinant inbred line (RIL) population of Arabidopsis thaliana that was grown using a hydroponic system with contrasted mineral nutrient supplies. QTL for growth related and biochemical traits were detected in each condition. Furthermore, QTL involved in response of these traits to differences in nutrient supply were also detected. The genetic basis of these response QTL could be involved in the adaptation of the plant to the reduction in mineral nutrient supply. One of these QTL was mapped on the bottom of the chromosome five and was involved in the response of rosette weight to lowered potassium supply. In the present study, this response QTL was validated with near isogenic lines (NILs) that had a Kas-2 introgression only at the QTL position in an otherwise Ler genetic background. The NILs retained over 20% more rosette weight than Ler in response to the reduced potassium supply. The QTL was further characterized: its effect on growth was present in a wide range of reduced potassium supplies but was abolished in the presence of ammonium. Furthermore, the NILs showed generally higher potassium content in the rosette as well as a higher water loss than Ler. There was no difference in stomatal density between the NILs and Ler and it is therefore assumed that a differential regulation of stomata opening will cause the water loss difference. The QTL was fine mapped to a ca 3.9 Mbp region and the response phenotype of different recombinant lines suggested that several interacting genes led to the observed effect of the QTL on growth in response to potassium reduction. The selection of candidate genes, underlying the effect of the QTL, is discussed and amongst others the potassium channel TPK1. Identification of the genetic and molecular basis of this QTL may shed light on a new regulatory mechanism that influences plant growth in response to potassium starvation and confers higher potassium efficiency to plants.
The Social Dimensions of Climate Change. Equity and Vulnerability in a Warming World. By R. Mearns, A. Norton and E. Cameron. Washington DC: The World Bank (2010), pp. 232, £25.00. ISBN 978-0-8213-7887-8.

If you have even the slightest interest in climate change, read this thoughtful, rigorous, and enlightening book! It is simultaneously a primer on vulnerability, a road map to climate change as a social justice issue (not just an environmental one) and its policy implications, and a sourcebook on some key indicators of vulnerability. Informed by theory and grounded in empirical data, the authors lay out multiple paths into understanding the ‘relationship between climate change and the key social dimensions of vulnerability, social justice and equity’. With a keen attention to difference and the importance of context, they explore questions of climate change at multiple scales, to different genders and their intersections, and in varying contexts including indigenous knowledge systems, cities, drylands, forests, armed conflict and policy formation. The brevity of the chapter on gender highlights the crucial need for additional and more careful work in this arena. Multiple chapters debunk popularly held assertions based on inappropriate research designs, crucial missing data, conjecture and worst case scenarios. For example, Clionadlh Raleigh and Lisa Jordan meticulously demonstrate why ‘environmental refugee’ is not a useful concept. Data on the geographical distribution of different environmental hazards and their consequences make clear the importance of context in addressing climate change. Jesse Ribot’s phrase, ‘vulnerability does not fall from the sky’, provides an evocative take home message. Vulnerability to climate change damage is created on the ground by governments, economic systems, and unequal social relationships of power and representation not just by biophysical factors.
Genetic Diversity of Vibrio parahaemolyticus from Narragansett Bay and Coastal Ponds of Rhode Island

ABSTRACT Quantitative polymerase chain reaction studies have detected Vibrioparahaemolyticus virulence genes (hemolysins tdh and trh) in Rhode Island oysters and waters. Illness caused by V. parahaemolyticus is currently rare in Rhode Island; however, there is concern over increasing aquaculture and water temperatures. The aim of this study was to characterize further the genetic diversity of V. parahaemolyticus in Rhode Island to determine disease risk. The genetic profile of pathogenic (tdh+ and/or trh+) strains and environmental (tdh-/trh-) strains of V. parahaemolyticus isolated from Rhode Island oyster and water samples was compared with pandemic and clinical strains using repetitive extragenic palindromic polymerase chain reaction. Of the 291 V. parahaemolyticus colonies isolated, 27 were pathogenic strains, with 25 of 291 (9.0%), tdh-/trh+; 1 of 291 (0.3%), tdh+/trh+; and 1 of 291 (0.3%), tdh+/trh-. Rhode Island isolates did not cluster closely with pandemic or clinical strains. Isolates containing tdh and/or trh genes from Rhode Island waters were predominantly tdh-/trh+, in contrast with a predominance of tdh+/trh- or tdh+/trh+ strains in Alaska, the Pacific Northwest, and the Gulf of Mexico. Similar to other studies in the United States, a high level of genetic diversity in pathogenic and environmental strains of V. parahaemolyticus was seen. This study clarified the diversity and virulence gene content (tdh and trh status) of V. parahaemolyticus isolates from Rhode Island waters.
The temporal-spatial pattern of vertical migration by the freshwater copepod Skistodiaptomus oregonensis relative to predation risk

La migration verticale de Skistodiaptomus oregonensis dans les lacs Kennedy et Paxton pourrait etre une adaptation permettant d'eviter un predateur, l'epinoche a trois epines (Gasterosteus aculeatus). Dans le lac Kennedy, deux autres especes predatrices, le saumon rouge (Oncorhynchus nerka) et le mysidace Neomysis mercedis pourraient egalement etre a l'origine du phenomene des migrations verticales. L'hypothese selon laquelle la migration verticale est due a la predation a notamment pour corollaire que l'ampleur de la migration et le moment ou elle survient reduisent le risque de predation. Nous avons teste ce corollaire pour chacune des especes susceptibles de chasser S. oregonensis. Des experiences en laboratoire ont permis de determiner que l'activite predatrice de l'epinoche diminue lorsque l'intensite lumineuse est inferieure a 1,6 μE. s -1 . m -2 . Le jour, dans les lacs Kennedy et Paxton, S. oregonensis se trouve a des profondeurs ou l'intensite lumineuse est inferieure a cette valeur. En outre, en montant vers la surface, au crepuscule, et en descendant en profondeur, a l'aube, demeure dans des conditions d'intensite lumineuse reduisant 'activite predatrice de 'epinoche. Si 'on en juge d'apres les donnees d'hydroacoustique et les publications sur l'alimentation du saumon rouge, dans le lac Kennedy les saumons rouges juveniles remontent vers les eaux de surface pour se nourrir avant le lever et apres le coucher du soleil. Or, les populations de S. oregonensis qui migrent a la verticale se trouvent pres de la surface de l'eau au crepuscule, lorsque les saumons juveniles remontent se nourrir. Par ailleurs, le moment ou S. oregonensis migre ne reduit pas la duree de son contact avec l'espece predatrice N. mercedis.
Impact of selected herbal products on intestinal epithelial permeation and metabolism of indinavir

Patients on anti-retroviral (ARV) drug treatment are sometimes simultaneously taking other prescribed drugs and/or over-the-counter drugs and/or herbal remedies. Pharmacokinetic drug-drug or herb-drug interactions can occur in these patients, which might be synergistic or antagonistic in nature leading to increased or decreased bioavailability of the ARV. Consequences of bioavailability changes may either be adverse effects due to increased plasma levels, or lack of pharmacological responses due to decreased plasma levels. The aim of this study is to determine if pharmacokinetic interactions exist between selected commercially available herbal products, namely Linctagon Forte, Viral Choice and Canova and the ARV, indinavir, in terms of transport and metabolism in cell culture models. Bi-directional transport of indinavir was evaluated across Caco-2 cell monolayers in four experimental groups, namely indinavir alone (200 μM, negative control group), indinavir in combination with Linctagon Forte, indinavir in combination with Viral Choice and indinavir in combination with Canova at three different concentrations. Verapamil (100 μM), a known P-gp inhibitor, was combined with indinavir in the positive control group. Samples obtained from the transport studies were analysed by means of a validated high performance liquid chromatography (HPLC) method. The apparent permeability coefficient (Papp) values were calculated from the transport results in both directions and the efflux ratio (ER) values were calculated from these Papp values. The metabolism of indinavir was determined in LS180 cells in the same groups as mentioned for the transport study but with ketoconazole (40 μM), a known CYP3A4 inhibitor, as the positive control group. Indinavir and its predominant metabolite (M6) were analysed in the metabolism samples by means of liquid chromatography linked to mass spectroscopy (LC/MS/MS) to determine the effect of the herbal products on the biotransformation of indinavir. The BL-AP transport of indinavir increased in a concentration dependent way in the presence of Linctagon Forte and Viral Choice when compared to that of indinavir alone (control group). Canova only slightly affected the efflux of indinavir compared to that of the control group. Noticeable increases in the efflux ratio values of indinavir were found for
Epstein‐Barr virus‐infected T cells in infectious monoucleosis

Epstein-Barr virus (EBV) has been known as a B cell lymphotropic virus since the initial discovery of this virus in the cell lines established from Burkitt’s lymphoma (BL). ’ EBV has been shown to cause infectious mononucleosis (IM), to be associated with BL and nasopharyngeal carcinoma, and to be linked to other neoplasms and polyclonal lymphoproliferative disorders in immunocompromized individuak2 EBV infects B lymphocytes by attachment to a cell surface receptor (c3d) of target cells. Some of these lymphocytes productively infected with EBV undergo lysis and do not survive, but others latently infected become immortalized and acquire the capacity to proliferate. EBV had not been thought to be associated with T cell lymphoma but recently the EBV genomes have been detected in neoplastic T cells, many of which expressed the CD8 p h e n ~ t y p e . ~ ~ We examined the lymph nodes of four patients with IM to determine the phenotypic expression of EBV-infected lymphocytes. Paraffin sections (3pm) were first stained by immunohistochemistry (IHC) using the alkaline phosphatase (ALP)-labeled avidin method employing primary antibodies of L26 (DAKO) as a B cell marker, CD3 (DAKO) as well as UCHL-1 (DAKO) as a T cell marker. They were stained bright red by the ALP reaction with naphthol-AS-BI phosphoric acid as a substrate and hexazotized new fuchsin as a coupler. In situ hybridization (ISH) was then performed using a digoxigenin-labeled oligonucleotide antisense probe for EBVencoded small RNA (EBER-1). The sections were treated with anti-digoxigenin alkaline phosphatase-conjugated antibody and then visualized with 5-bromo-4-chloro-3-indolyl phosphate (BCIP) and nitroblue tetrazorium salt (NTB) to produce purple-black signals. The sense probe and specimens of EBV-negative lymphadenitis were used as controls and gave completely negative results.
Effective number of genes and accuracy of genomic evaluations

In this study we estimated the distribution of genetic variance for production and fertility traits across chromosomes, and used this information to calculate the effective number of genes associated to these traits. The estimated numbers of genes were then used in order to assess and to compare the expected accuracies of genomic evaluation using either GBLUP or BayesB. The regression of the proportion of genetic variance attributed to each autosome on its physical length fitted very well a linear relationship for all traits. The estimated effective number of genes ranged from ~400 (for fat percentage and non-return rate) to ~1000 (for milk yield, interval from calving to first insemination and days open). Our results provide evidence that a large number of genes is involved in the inheritance of milk production and fertility traits in dairy cattle. Expected accuracies of genomic predictions ranged from 0.76 to 0.87 for fertility traits, and from 0.83 to 0.92 for production traits. Expected accuracies of genomic evaluation were higher with BayesB for traits with lower number of QTL, and with GBLUP for larger number of QTL.
Adaptogenic potentials of Camellia sinensis leaves, Garcinia kola and Kola nitida seeds

In this study, we screened Garcinia kola seed (GKS), Kola nitida seed (KNS) and Camellia sinensis Leaves (TEA) for adaptogenic potentials. The investigation was carried out in albino rats to determine the ability of these plant materials to increase non-specific resistance against physical, chemical and biological stressors. The results show that the three plant materials protected the animals from bacteria-induced mortality and morbidity and significantly reduced infection-induced leucocytosis in the rats. This confirms the ability of the herbs to protect the organisms from biological stress. However, while GKS was more effective than the other adaptogens in reducing monocytosis, KNS and TEA were effective in reducing neutropenia. Only KNS alleviated lymphocytosis. The effect of the adaptogens in alleviating physical stress was evaluated by the cold immobilization stress-induced ulcer models. The three adaptogens significantly (P GKS > TEA. The result shows that G. kola seed (GKS) alleviated the hepatic degenerative changes associated with ciprofloxacin. G. kola seed, K. nitida seed, and C. sinensis leaves have shown remarkable ability to increase non-specific resistance to biologic, physical and chemical stressors and could therefore qualify as adaptogens.
Muscle hypertrophy induced by myostatin inhibition : a new therapeutic approach of muscle atrophy

Increasing size and strength of skeletal muscle represents a promising therapeutic strategy for muscular disorders. One possible new tool is Myostatin (Mstn) because it plays a crucial role in regulating skeletal muscle mass. The first goal of our work was to determine whether Mstn inhibition could prevent muscle atrophy in catabolic states. As glucocorticoids play a major role in most muscle atrophy models, we assessed whether muscle atrophy caused by glucocorticoids in excess could be prevented by Mstn inhibition. This hypothesis was suggested by the fact that glucocorticoids increase muscle Mstn expression and that Mstn muscle overexpression is sufficient to cause muscle atrophy. Our work showed that deletion of Mstn gene protects skeletal muscle from glucocorticoid-induced atrophy, partially through inhibition of proteolysis. The identification of Mstn binding proteins able to inhibit Mstn activity has led to potential new approaches for postdevelopmental muscle mass enhancement. These Mstn binding proteins include Follistatin (FS) which shows a potent Mstn-inhibiting activity. The increase in muscle mass observed in transgenic mice overexpressing FS in muscle is even significantly larger than that observed in Mstn KO mice, suggesting that other ligands could contribute to the muscle hypertrophic effect of FS. The mechanisms involved in the FS effect are however relatively unknown. The second aim of this thesis was to investigate the contribution of satellite cells to the FS-induced muscle hypertrophy and to assess whether other FS ligands could act similarly to Mstn in controlling muscle growth. Our study showed that FS overexpression induces skeletal muscle hypertrophy via satellite cell activation and probably increased protein synthesis. Furthermore, our results indicate that FS-induced hypertrophy results not only from Mstn but also from Act inhibition. These observations therefore suggest that, besides Mstn, Act is a crucial player in the regulation of muscle mass. In conclusion, this work demonstrates the interest and the feasibility of Mstn inhibition as a potential therapeutic approach in muscle wasting disease. Since Mstn gene deletion prevents the muscle atrophy caused by dexamethasone and glucocorticoids are involved in muscle atrophy observed in many catabolic conditions, Mstn inhibition may be helpful in the treatment of disease-related muscle loss. Among Mstn inhibitors, FS seems to be a promising tool because of its powerful hypertrophic effect on skeletal muscle mass. As we showed, its anabolic action results from inhibition of both Mstn and Act, which negatively regulate muscle growth.
Development and application of cryo-cell-UV-laser ablation mass spectrometry (UV-LA-ICPMS) to Greenland Ice cores : implications for abrupt climate change and ice physics

Ice cores from Greenland preserve a continuous ~125 kyrs record of climate change at very high resolution. The most remarkable of these changes are Dansgaard-Oeschger (DO) cycles, which are characterized by very rapid Greenland temperature shifts of 5-16°C recorded in δO and reflected in many other proxies such as dust (Ca, Al, Fe) and sea salt (Na, Mg). DO events also are recorded in other northern and southern hemisphere archives such as speleothems and thus show the large-scale extent of these climate variations. By applying cryo-cell UV-LA-ICPMS (Ultra-Violet Laser-Ablation InductivelyCoupled-Plasma-Mass-Spectrometry) directly to frozen NGRIP ice samples, we investigated elemental proxies of dust and sea salt at an unprecedented spatial resolution of ≤200 μm while maintaining ppb detection limits. For the investigated DO event 22 (87.6-84.7 ka), we thus achieve approximately bimonthly time resolution. Using a series of suitably homogenous reference ice standards specifically prepared during this project, fully quantitative external concentration calibration is achieved. This high resolution dataset for the main GS22 transitions as well the GS21 precursor shows (1) the phasing of dust, sea salt and temperature proxies, where dust precedes temperature change by three to ten years, (2) the ~tenfold change in dust concentrations within one year at the GS21.2 and GI21 warming events, (3) a transient phase from interstadial to stadial lasting several decades and characterized by high amplitude oscillations before the onset of the cold/warm phase (‘flickering of climate signal’), (4) the confirmation that dust and sea salt proxies vary significantly even during minor precursor climatic events, and (5) the quantification of rapid changes in dust provenance as deduced from elemental ratio signatures. We also investigated the role of soluble and insoluble impurities during ice grain growth and recrystallization, and show that impurities distribute preferentially on grain boundaries for relatively low concentration ice but not for ‘dirtier’ ice. This difference is interpreted to be related to the size of impurities. While in clear ice impurities are mostly mobile soluble micro-inclusions with sub-micron dimensions that are easily harvested by moving boundaries, in impurities-enriched layers (cloudybands) large insoluble particles prevail, reducing the mobility of grain boundaries. Table of
Dietary selection of protein and energy by pullets and broilers

1. White Leghorn pullets and sexed broilers were allowed a free choice of two “ split‐diets “ which were concentrated sources of either crude protein (463 g/kg diet) or energy (13.32 to 14.00 MJ/kg diet). 2. Pullets receiving these two diets displayed a slower, but more uniform growth rate than did birds offered a single conventional diet. Up to 11 weeks of age, control birds consumed significantly more protein while the converse was true from 11 to 20 weeks. These differences are discussed in relation to the stage of sexual maturity. 3. Broilers offered the split‐diets grew more slowly and had an inferior food conversion ratio compared with control birds fed on a two‐stage rearing programme. 4. Among the broilers offered split‐diets, the usual sex differences were not observed for weight gain or carcass fat content.
Breeding and Genetics : ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines

The objective of this study was to determine genetic variation of five Korean native chicken lines using 30 microsatellite(MS) markers, which were previously recommended by ISAG(International Society for Animal Genetics). The initial study indicated that two microsatellite markers, MCW0284 and LEI0192, were not amplified in these lines and excluded for further analysis. Twenty eight microsatellite markers were investigated in 83 birds from five Korean native chicken lines. The identified mean number of alleles was 4.57. Also, the expected, observed heterozygosity(He, Ho) and polymorphism information content(PIC) values were estimated in these markers and they ranged from 0.31~0.868, 0.145~0.699, and 0.268~0.847, respectively. The results were used for the discrimination of five chicken lines using genetic distance values and also neighbor-joining phylogenetic tree was constructed. Based on the He and PIC values, eighteen markers are enough for the discrimination of these Korean native chicken lines for the expected probability of identity values among genotypes of random individuals(PI), random half sibs(PIhalf-sibs) and random sibs(PIsibs). Taken together, these results will help the decision of conservation strategies and establishment of traceability system in this native chicken breed. Also, the use of ISAG-recommended microsatellite markers may indicate that the global comparison with other chicken breeds is possible.
Osteogenic activities of MC3T3-E1 cells on heparin-immobilized poly(caprolactone) membranes

The aim of this study was to investigate the effects of heparin on the activity of osteoblast-like cells seeded on poly(caprolactone) (PCL) membranes. The membranes were prepared by solvent-casting technique in ~150 µm thickness. Then they were treated with 1,6-hexanediamine solution and functionalized with covalently bound heparin. The morphology, proliferation, and differentiation of MC3T3-E1 preosteoblasts on these membranes were investigated in vitro. The heparin functionalized PCL membranes, compared to non-functionalized membranes, significantly stimulated osteoblast proliferation. The Scanning electron microscope images confirmed the stimulative effect of covalently bound heparin on the osteoblast-like cell proliferation. The alkaline phosphatase and osteocalcin levels for cells proliferated on heparin containing PCL membranes were higher than that of nonfunctionalized membranes.