Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between the voracious heterotrophic nanoflagellate Katablepharis japonica and common heterotrophic protists

Copyright © 2017 The Korean Society of Phycology 309 http://e-algae.org pISSN: 1226-2617 eISSN: 2093-0860 Interactions between the voracious heterotrophic nanoflagellate Katablepharis japonica and common heterotrophic protists So Jin Kim, Hae Jin Jeong*, Se Hyeon Jang, Sung Yeon Lee and Tae Gyu Park School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea Advanced Institutes of Convergence Technology, Suwon 16229, Korea Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea
Étude transcriptomique des cellules dendritiques CD103+ CD4+ chez le rat transgénique HLA-B27, modèle de la spondylarthrite

La spondylarthrite (SpA) est l’un des rhumatismes inflammatoires chroniques les plus frequents et se caracterise par des manifestations articulaires et extra-articulaires particulieres. Chez le rat transgenique pour le HLA-B27 et la β2-microglobuline humaine, le developpement spontane d’une maladie proche de la SpA est fortement correle a un dysfonctionnement des cellules dendritiques (DC). Nous avons donc etudie les facteurs impliques dans ce dysfonctionnement en effectuant une analyse transcriptomique des DC spleniques CD103+ CD4+ a l'aide de puces pangenomiques. Cette etude a revele un defaut majeur de la voie de signalisation de l’interferon (IFN) dans les DC de rats HLA-B27, par la sous-expression de nombreux genes appartenant a cette voie. Nous avons compare nos resultats avec ceux rapportes dans des macrophages derives de monocytes de patients atteints de SpA. Cette meta-analyse a revele l’existence d’une signature inverse de l’IFN partagee entre les patients et les rats HLA-B27. Dans notre modele de rat, ce defaut a ensuite ete confirme puis replique sur des echantillons independants par PCR quantitative sur une selection de genes d’interet : l’Ifng, les chimiokines Cxcl9, Cxcl10 et Cxcl11 ainsi que les facteurs de transcription Stat1, Ifit2, Ifit3, Irf1 et Irf7. De plus, nous avons mis en evidence dans ces DC HLA-B27 une regulation positive de Socs3 qui pourrait expliquer ce defaut de signalisation via l’IFN, ainsi qu’une sous-expression des genes codant pour les interleukines IL-27 et IL-10, qui favoriserait l’expansion des lymphocytes Th17 pathogenes au detriment des cellules T regulatrices. Enfin, plusieurs genes impliques dans le stress du reticulum endoplasmique tels que Calr, Pdia4 et Pdia6 apparaissent surexprimes dans les DC de rats HLA-B27. L’ensemble de ces resultats suggere que l’expression du HLA-B27 dans les DC spleniques CD103+ CD4+ pourrait etre a l’origine de la signalisation defectueuse de l’IFN, et ainsi jouer un role dans la pathogenese de la SpA.
The zoonotic pathogen Helicobacter heilmannii from feline origin : aspects of virulence and gastric colonization

Gastrale Helicobacter species, afkomstig van dieren, kunnen net zoals de typisch humane bacterie Helicobacter pylori de maag van de mens koloniseren en ziekte veroorzaken. Deze zogenaamde niet-H. pylori Helicobacter species (NHPH) werden reeds geassocieerd met gastritis, maagulcera en mucosa-geassocieerde-lymfoid-weefsel (MALT) lymfomen. Bovendien is het risico op het ontwikkelen van MALT lymfomen hoger na een infectie met gastrale NHPH dan met H. pylori. NHPH omvatten een groep van nauwverwante maar verschillende Helicobacter species die worden teruggevonden in verschillende diersoorten. Zo koloniseren H. felis, H. salomonis, H. bizzozeronii, H. heilmannii, H. cynogastricus en H. baculiformis de maag van hond en kat, terwijl H. suis voornamelijk wordt teruggevonden in varkens. Gastrale NHPH zijn bijzonder moeilijk te kweken in het laboratorium, waardoor er wereldwijd maar weinig in vitro isolaten beschikbaar zijn. H. heilmannii werd in 2011 voor het eerst succesvol geisoleerd uit kattenmagen en in vitro in cultuur gebracht. Dit doctoraatsonderzoek had tot doel om een beter inzicht te verwerven in de pathogenese van maaginfecties met H. heilmannii, om de mogelijke virulentiefactoren van H. heilmannii in kaart te brengen en om het repertoire aan buitenste membraan-proteinen van deze kiem te vergelijken met deze van andere gastrale Helicobacter species.
A practical guide to insect cell cultures: establishment and maintenance of primary cell cultures

In the last three decades several insect species have been studied in vitro using cell culture revealing fundamental information about their biology. However, numerous important species have never been investigated at a cellular level so that insect cell culture is still in an early stage of its potential development. In the present review, we summarized the main steps involved in the establishment of primary cell cultures to serve as a practical guide for current and future entomologists to leverage the power of cell cultures. This approach has the potential to generate valuable results and suggestions about insect metabolism, vectorial capacity and adaptation to different stresses and challenges. Although most published papers discussed immortalized cell lines, we focussed our review on primary cell culture since they can give precise data in different research fields.
Magnitude and mechanism of siderophore-mediated competition in bacterial interactions

Whether microbial interactions are predominantly cooperative or competitive is a central question in microbial ecology, and determines the composition and stability of microbial communities. The secretion of iron chelators called siderophores is a model system for cooperative interactions, even though these chelators can also mediate competition by depriving competitors of iron. Using a genetically engineered experimental system based on the Pseudomonas aeruginosa siderophore pyochelin, we found that secreting siderophores to inhibit a competitor can lead to higher benefits than secreting siderophores to make iron available. Based on thermodynamic modeling, we propose that competitive inhibition by siderophores is efficient in kinetically controlled saturated systems, where dissolution of precipitated iron phases is slow. Under these conditions, met in many natural environments, secreted siderophores temporarily reduce the concentration of available iron and can thus induce growth inhibition in a competing strain, even at high iron concentrations. These findings give insight into the function of siderophores: In addition to its cooperative nature, siderophore secretion could also be a widespread mechanism for mediating competitive interactions. Our functional investigation reveals a complexity in microbial interaction networks that would remain hidden when focusing on genomic information alone.
Species relationships in the dasyurid marsupial genus Pseudantechinus (Marsupialia : Dasyuridae): a re-examination of the taxonomic status of Pseudantechinus roryi

Abstract. The status of Pseudantechinus roryi relative to its congeners has been determined from DNA sequences obtained from both nuclear and mitochondrial gene loci. Although all other recognised species of Pseudantechinus form reciprocally monophyletic lineages in phylogenetic analyses, individuals identified in museum collections as Ps. roryi (including type specimens) were indistinguishable from those identified as Ps. macdonnellensis. Ps. roryi is thus considered to be a synonym of Ps. macdonnellensis. Neighbour-joining network analyses failed to reveal any clear biogeographic differences between populations of Ps. macdonnellensis other than some evidence of isolation by distance.
Control of biogas production process by enzymatic and fluorescent image analysis

ABSTRACT The process of methanogenesis, which is in the essence of the widely distributed technologies for biogas production, is slow, has multiple steps and occurs under anaerobic conditions. These factors make the control and the management of the anaerobic digestion difficult and impose the testing and implementation of new indicators for control which are fast and focused on the activity and functioning of the methanogenic community in addition to the traditionally used technological parameters. In this study, the biogas production process in wastewater treatment plant ‘Kubratovo’ was analysed in two different seasonal situations and a correlation was made between the studied parameters for control. The complex methodological arsenal included the activities of aerobic and anaerobic dehydrogenase, fluorescent image analysis and key chemical and technological indicators. The correlation analysis showed that the fluorescent image analysis parameters (number/mean size of clusters; fluorescence intensity; area) had the strongest relationship with the biogas production. Based on these results, we propose a fluorescent indicative system for control of the biogas production technologies. It is a fast tool for assessment the effectiveness of the process of anaerobic digestion. Its focus on the activity and functioning of the biological system could contribute to the optimization of the whole performance of these technologies and could serve as a prediction tool for potential problems in the future.
Cattle manure biochar potential for ameliorating soil physical characteristics and spinach response under drought

ABSTRACT Drought and low amounts of organic matter are two main constraints in arid and semiarid regions and their adverse effects on soils and plants can be alleviated by biochar (B). Therefore, the influence of 0 (0B), 1.25 (1.25B), 2.5 (2.5B) and 5% (5B) cattle-manure biochar on the growth and physiological traits of spinach and physical characteristics of postharvest soil under field capacity (FC), 0.7FC and 0.55FC conditions was evaluated. Drought decreased stomatal conductance (SC), water use efficiency (WUE), shoot dry matter yield (SDMY), soil water repellency (WR) and saturated hydraulic conductivity (Ks) by 13–45%, 3–17%, 27–51%, 48–60% and 26–36%, respectively. Whereas, all B treatments increased SC, Ks and total porosity by 11–63%, 82–221% and 2–12%, respectively. Application of 1.25B increased SDMY and WUE, whereas higher B levels were ineffective, i.e. 2.5B did not significantly affect the measured parameters and 5B reduced them. At all B levels, drought reduced SDMY. However, the lowest decrease in SDMY was observed by 1.25B. Despite their positive influence on soil’s physical quality, high B levels induced excessive salinity. Therefore, a low B level (1.25B) may be recommended since it provides positive impacts on the plant’s growth and yield while mitigating the adverse effects of drought.
Effects of human traffic on use of trails by mammals in lowland forest of eastern Ecuador

Human activity can lead to changes in animal behavior and distribution patterns if the level of activity is high enough to cause disturbance. Both humans and other animals commonly use human-made trails in lowland tropical forest and, therefore, it is possible that use of trails by humans might affect the likelihood that animals would use those same trails. We investigated this possibility at a site in lowland forest of eastern Ecuador using camera traps to document numbers of people and numbers of other animals at a series of camera locations during January–March, 2014–2016. Human activity was higher on trails used by all visitors to the research station than on two research plots where human activity is restricted. Ungulates were the only group to show a strong negative relationship with human activity but only on trails open to all visitors; there was no apparent negative impact of human activity on research plots. Results suggest that the level of human activity along trails is not now causing negative impacts to most mammals but also that levels of activity should be monitored to ensure that any increase in human presence does not lead to negative responses by mammals.
Leakage of forest harvest changes in a small open economy: case Norway

ABSTRACT The effect of changes in roundwood harvests in Norway on the harvests in rest of the world is examined using a global forest sector model. About 60–100% of the harvest change in Norway is offset by an opposite change in the rest of the world. Such leakage rates vary over time, wood category, background scenario, and the size of the harvest change. Asymmetries between the effects of increasing and decreasing the harvests also exist. Hence, the magnitude of leakage rate is case specific, though considerable. Under tightening wood supply there is less need/room to respond to harvest increase/decrease in Norway with incremental/reduced harvests elsewhere. When the use of global forest resources intensifies with increasing wood demand in the future, leakage rates can be smaller than today. It is important to account for harvest leakage in order to avoid overestimating the climate benefits of policies that decrease or increase roundwood harvests. For instance, for full carbon sequestration benefits of increasing harvests for harvested wood products, creating fresh additional demand for these products should be prioritized. Else the origin of raw material and the place of production for these products may change instead of their stock.
Agressividade do patógeno Phaeocytostroma ambiguum causando podridão de colmo em milho.

1Estudante Engenharia Agronômica Universidade Feder al de São João del-Rei, Sete Lagoas, Minas Gerais; 2 Pó doutorando em Fitopatologia, Embrapa Milho e Sorgo, Sete Lagoas, Minas Gerais; frederick.aguiar@colaborador.embrapa.br e briciolan za@gmail.com; Pesquisador(a), Embrapa Milho e Sorgo, Sete Lagoas, Minas Gerais, dagma.silva@embrapa.br e luci ano.cota@embrapa.br; Graduando em Engenharia Ambiental, Faculdades Santo Agostinho/ FASASETE, Sete Lagoas, Minas Gerais;
Diferensiasi Stadium Takizoit-Bradizoit pada Toxoplasma gondii

Toxoplasma gondii is an intracellular parasite whose definite host is cat or felidae and intermediate host is human or other mammals. It causes congenital and acquisita toxoplasmosis. Infection with this apicomplexan parasite results in its dissemination throughout its host via the tachyzoite life stage. After dissemination, these tachyzoites differentiate into bradyzoites within cyst and remain latent. These bradyzoites can transform back into tachyzoites and in immunosupressed individuals this often results in symptomatic disease. Both tachyzoites and bradyzoites develop in tissue culture and this crucial differentiation event can be studied. Interferon gamma (IFN ) is the main mediator in tachyzoite-bradyzoite differentiation.
Evaluacion del exito reproductivo de armeria caespitosa en el contexto de cambio climatico en la alta montaña mediterranea

RESUMEN: La informacion obtenida sobre diferentes aspectos del ciclo vital de Armeria caespitosa sugiere que la especie tiene capacidad para vivir bajo condiciones ambientales muy diferentes. A. caespitosa es capaz de ocupar y reproducirse de manera fructifera en dos microhabitats contrastados a lo largo del gradiente altitudinal que ocupa. La especie tiene ademas flexibilidad para reclutar nuevas plantulas en los extremos de su gradiente altitudinal. Parece, ademas, que A. caespitosa adopta, tambien de manera exitosa, distintas estrategias demograficas como respuesta a las diferentes condiciones ambientales en los extremos del gradiente altitudinal. Estas caracteristicas en conjunto implican que la especie tiene potencial y flexibilidad para mantener poblaciones viables bajo las nuevas condiciones que impondra el cambio climatico actual.
Adapting trace mineral nutrition of birds for optimising the environment and poultry product quality

In the past, trace minerals have been inadequately considered by poultry nutritionists, as demonstrated by the scarce availability of literature. The practice of using high safety margins between requirements and dietary concentrations and the relative low cost of these essential minerals are possible reasons for this. Environmental considerations and regulations limiting trace mineral supply and improvements in analytical methods to detect putative contaminants in mineral sources have led to a need to a re-examination of trace mineral requirements. In addition, new knowledge regarding trace mineral roles in bone metabolism, anti-oxidant status, homeostatic regulation, product quality, immunology and the development of novel trace mineral sources have favoured, for the past 15 years, interests in optimising trace mineral nutrition considering other parameters than solely the bird performance. This review analyses the role of essential trace minerals (mainly Zn, Cu, Fe, Mn, I, Se) in broiler and laying hen nutrition. This work aims to highlight the evaluation of trace mineral requirement, the bioavailability of trace mineral sources, especially in regards with phytate antagonism, and the main functions of trace minerals in egg, eggshell and meat quality. The impact of trace minerals on the environment (toxicity to plants and microorganisms) is considered and nutritional means to reduce the risk of environmental contamination will be explored. Finally, the possibilities of poultry product's enrichment in some trace minerals for the benefit of human health will be explored.
Stranded capital: environmental stewardship is part of the economy, too

The many values that humans place on biodiversity are widely acknowledged but difficult to measure in practice. We address this problem by quantifying the contribution of marine-related environmental stewardship, in the form of donations and volunteer hours, to the economy of coastal Massachusetts. Our conservative evaluation suggests that marine stewardship activities contributed at least $179 million to the state economy in 2014, a figure that exceeded revenues derived in that same year from commercial finfish operations ($105 million) and whale watching ($111 million), two acknowledged cornerstones of the regional economy. Almost imperceptibly, the coastal economy has been transformed from one dependent on commercial exchange to a diverse economy that includes, to a large measure, marine stewardship. Donations and volunteer efforts are useful indicators of environmental values that can be hard to quantify, and represent one measure of human determination to protect the planet.
Antibacterial and antifungal effects of the leaf, seed, seed coat and fruit capsule of Aesculus hippocastanum (Sapindaceae) extracts

The present study describes the antimicrobial activity of the leaf, seed, seed coat and fruit capsule of horse-chestnut ( Aesculus hippocastanum , L.) extracts from the Ordu Province of Turkey. These extracts were first prepared with ethanol solvent. The antimicrobial activity of the extracts was then assessed using the disc diffusion method against 7 bacteria and 1 yeast. The antimicrobial test results revealed that each the crude extracts of A. hippocastanum exhibited very weakly possess antibacterial activity in the case of both Gram-positive and Gram-negative bacteria. The most sensitive microorganism to A. hippocastanum samples were Proteus vulgaris and Listeria monocytogenes . The results presented in this paper suggest the possibility that A. hippocastanum possesses a new antimicrobial compound that has a weakly effect against some Gram-negative and Gram-positive bacteria, but did not against fungi.
Relation avec la sécrétion lactée. Évolution de l’activité métabolique du tissu adipeux chez la chèvre au cours des deux premiers mois de lactation

Le poids de l'épiploon (rapporté au DNA) de 5 chèvres en 9semaine de lactation est en relation inverse avec la quantité de lait produite au cours des 2 premiers mois de lactation. Cette relation semble résulter d'un dépôt de lipides dans le tissu adipeux, d'autant plus précoce que les animaux produisent moins de lait. L'activité de 4 enzymes lipogéniques et la monoinsaturation des acides gras de l'épiploon tendent par ailleurs à augmenter chez 4 des 5 chèvres, entre la 3e et la 9e semaine de lactation.
Using multiple satellite observations to quantitatively assess and model oil pollution and predict risks and consequences to shoreline from oil platforms in the Caspian Sea

ABSTRACT This research focused on the following objectives: (1) using satellite data to characterize the spatiotemporal distribution of anthropogenic oil spills from Oil Rocks Settlement, Chilov and Pirallahi Islands (2) stochastic modeling of the oil spill risk pose to water quality and shoreline ecosystems, and (3) validating model predictions using satellite images. 165 satellite images acquired by SENTINEL-1A, LANDSAT-8, RADARSAT, ENVISAT and ERS sensors between 1996 and 2015 were used for the detection of oil spills using object-based classification and visual interpretation. Anthropogenic hotspots were observed at three oldest oil production sites with estimated oil spilling up to 1264 m3 per day and different degrees of temporal repetition of oil spills. The largest area (5639 km2) experienced 1–10 detected oil spills, while 993 km2 experienced 11–20 oil spills, 775 km2 experienced 21–50 oil spills, 208 km2 experienced 51–100 oil spills, and 36 km2 experienced 101–150 oil spills. The majority (83% or 6157 km2) of sea surface area within the combined boundary of detected oil spills (7422 km2) had a 50% or greater chance of oil spill contamination. Approximately, 6% (44 km of 751 km) of shoreline had a 50% or greater probability of contamination with land use classes sensitive to pollution.
ISOLATION AND CHARACTERIZATION OF NEW MICROSATELLITE MARKERS FOR THE CORTÉS GEODUCK ( Panopea globosa )

The geoduck Panopea globosa is a long-lived and large endemic infaunal clam sustaining a growing fishery in the Northwest coast of Mexico that, in spite of its increasing demand in Asian markets very little is known about its biology. In order to provide genetic markers to support genetic research of wild populations, nine novel microsatellite loci (di-, tri-, and tetranucleotide repeats) were developed using shotgun sequencing with next generation technology (Illumina). The number of alleles per locus ranged from 3 to 16 and the observed and expected heterozygosity ranged from 0.286 to 0.650 and 0.504 to 0.906, respectively. Five loci were found to be significantly deviated from the Hardy-Weinberg equilibrium and three pairs showed evidence of linkage disequilibrium. Most loci are highly informative for population genetics and linkage analyses according to their polymorphism information content (> 0.5) and will be useful for increasing our understanding of the wild population structure and developing a sustainable fishery management. Aislamiento y caracterizacion de nuevos marcadores microsatelitales en la almeja generosa ( Panopea globosa ) La almeja generosa Panopea globosa es una especie infaunica longeva y de gran tamano que mantiene una pesqueria creciente en la costa del Noroeste de Mexico. A pesar de su demanda creciente en los mercados asiaticos, se conoce muy poco acerca de su biologia. Con la finalidad de proveer nuevos marcadores geneticos para la caracterizacion de poblaciones silvestres, se desarrollaron nueve marcadores microsatelitales nuevos (con patrones repetidos de di-, tri-, y tetranucleotidicos) utilizando secuenciacion genomica aleatoria con tecnologia de secuenciacion de siguiente generacion (Illumina). El numero de alelos por locus vario de 3 a 16 y los valores de heterocigosidad observada y esperada variaron de 0.286 a 0.650 y 0.504 a 0.906, respectivamente. Cinco microsatelites se desvian del equilibrio de Hardy-Weinberg y tres pares de microsatelites mostraron evidencia de desequilibrio de ligamiento. La mayoria de los loci son altamente informativos para estudios poblacionales y analisis de ligamiento de acuerdo con su contenido de informacion de polimorfismos (> 0.5) y seran utiles para incrementar el conocimiento de la estructura genetica de las poblaciones silvestres de esta almeja y para coadyuvar en su pesqueria sustentable.