Miracle-dz/UniFAR-FTUs huggingface dataset:
Les astrocytes, cellules relais des interactions neuro-immunes dans le système nerveux central

L’astrocyte joue un role preponderant dans la regulation des reponses immunes au sein du systeme nerveux central. Afin d’analyser les cascades moleculaires complexes suspectees de conduire a des atteintes neuroinflammatoires, nous avons etabli in vitro un modele d’interaction de lymphocytes T chroniquement actives avec des astrocytes humains (Dev-Ast), des astrocytes et oligodendrocytes de Rat en culture primaire, ou bien des precurseurs nerveux multipotents (lignee Dev). Nous montrons que les astrocytes humains et de Rat ont un profil reactif apres contact avec les lymphocytes T actives. Leur secretion de cytokines pro-inflammatoires est elevee et se traduit par une augmentation de leur expression de metalloproteases (MMP) et d’inhibiteurs endogenes specifiques (TIMP). Ces modulations sont retrouvees dans les precurseurs nerveux. L’alteration du systeme proteolytique MMP/TIMP est associee a une mort cellulaire induite par le contact lymphocytaire. Nous montrons que MMP et TIMP sont impliques dans les cascades de signalisation de mort. Les lymphocytes T actives induisent une apoptose des precurseurs nerveux, mediee par Fas et leur sensibilite a l’apoptose est potentialisee par des inhibiteurs de MMP. Une stabilisation de Fas en surface par une inhibition de son clivage via des TIMP est suspectee. Les lymphocytes T actives induisent egalement l’apoptose d’oligodendrocytes immatures presents dans la culture gliale mixte. Cette mort est associee a une alteration du systeme MMP/TIMP dans les astrocytes et est mediee par Fas dont l’expression est augmentee sur les oligodendrocytes. Ainsi, le dialogue etabli entre lymphocytes T actives et cellules nerveuses induit une cascade moleculaire impliquant les cytokines pro-inflammatoires et le systeme proteolytique MMP/TIMP. Dans ce dialogue, le relais astro- cytaire apparait comme crucial dans le processus qui conduit a la mort de cellules nerveuses. Une alteration du systeme MMP/TIMP detectee chez des patients developpant une atteinte neuroinflammatoire, la myelopathie associee a l’infection par le retrovirus HTLV-1, renforce cette hypothese.
Genetic Evaluation of Exotic Chromatins from Two Obsolete Interspecific Introgression Lines of Upland Cotton for Fiber Quality Improvement

Interspecific introgression lines are important resources for plant breeders to access novel alleles from exotic germplasm. The Pee Dee breeding program developed several extralong staple “Sealand” germplasm lines that presumably contain sea island cotton (Gossypium barbadense L.) chromatin introgressed into upland cotton (Gossypium hirsutum L.). The objectives of this study were to identify the G. barbadense chromatins in the Sealand lines, 542 and 883, and evaluate their effects on fiber quality. A total of 31 putative G. barbadense chromatins were detected, including 12 segments on seven chromosomes that were unique to Sealand 542 and 10 segments on five chromosomes that were unique to Sealand 883, and the remaining nine segments were common to both the Sealand lines. Sealand 542 and 883 mapping populations were created to identified 28 quantitative trait locus (QTL) regions associated with fiber quality traits, including six for elongation, four for fineness, five for short fiber content, five for strength, three for length, and five for fiber uniformity. At least 13 QTLs were detected on the G. barbadense introgressed chromosomal segments. Favorable alleles for 17 QTLs were contributed by the Sealand lines, and the genetic effects of five loci were stably expressed across environment and generation. Stable expression of G. barbadense fiber quality alleles in the Sealand lines and the absence of these alleles in upland germplasm make these introgression lines a valuable resource for fiber quality improvement. In particular, markerassisted introgression of the qFL-Chr25 locus from Sealand 883 should result in improved fiber length, whereas that of qMIC-Chr24 from Sealand 542 should result in finer fiber. P. Kumar, Cotton Molecular Breeding Lab. , Univ. of Georgia, Tifton, GA 31793, current address, USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA 93905; R. Singh, E.L. Lubbers, and P.W. Chee, Cotton Molecular Breeding Lab. , Univ. of Georgia, Tifton, GA 31793; X. Shen, Cotton Molecular Breeding Lab. , Univ. of Georgia, Tifton, GA 31793, current address, Biotechnology Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; A.H. Paterson, Plant Genome Mapping Lab. , Univ. of Georgia, Athens, GA 30606; B.T. Campbell, USDA-ARS Coastal Plains Soil, Water and Plant Research Center, 2611 W. Lucas St., Florence, SC 29501; D.C. Jones, Cotton Incorporated, 6399 Weston Parkway, Cary, NC 27513. Received 12 Dec. 2018. Accepted 12 Feb. 2019. *Corresponding author (pwchee@uga.edu). Assigned to Associate Editor Linghe Zeng. Abbreviations: GRIN, Germplasm Resources Information Network; LOD, logarithm of odds; PCR, polymerase chain reaction; PV%, percentage phenotypic variation; QTL, quantitative trait locus; SSR, simple sequence repeat. Published in Crop Sci. 59:1073–1084 (2019). doi: 10.2135/cropsci2018.12. 0745 © 2019 The Author(s). Re-use requires permission from the publisher. Published May 16, 2019
Effects of wood decay by Heterobasidion annosum on the vulnerability of Norway spruce stands to wind damage: a mechanistic modelling approach

The increase of wood decay due to the fungal pathogen Heterobasidion annosum is expected to increase the vulnerability of tree stands to wind damage due to the decrease in tree anchorage (by wood decay in roots) and stem strength (by wood decay in stem wood). In this work, we developed a framework to simulate the effects of wood decay by Heterobasidion annosum on the vulnerability of Norway spruce (Picea abies (L.) Karst. ) stands to wind damage in terms of uprooting and stem breakage. We also demonstrated the model performance by using tree- and stand-level sensitivity analyses. The increase in the amount of wood decay decreased the predicted wind speeds needed for both uprooting and stem breakage of trees and increased the predicted amount of wind damage. The probability of uprooting was higher than stem breakage for infected trees, which was opposite to the findings for the healthy trees. Because of some simplifications in the modelling due to the lack of proper experimental data (e.g., effects of wood .
Comparative Evaluation Of Anticancer Potential Of Moringaoleifera, Ganodermalucidumand Silver Nanoparticles Against Breast And Liver Cancer Cell Lines And Related Pro And Anti Apoptotic Genes Profile

The present work aimed to evaluate the anticancer potentials concerning the cytotoxicity and antiproliferative activity of L-amino acid Oxidase (LAAO) ,MoringaOleifera(MO) Methanol (MLM) and water extracts (MLW), Ganodermalucidum(GL), extracts as a natural products and Silver nanoparticles (AgNP) as well. Cytotoxic effect of test extracts on both breast (MCF-7) and liver(HEPG-2) cancer cell lines varied according to test materials and could be arranged in the order of LAAO > MLM>AgNP> GL>MLW. Also, (MCF7) cell line was more sensitive to test materials compared with (HEPG2) cell line. Regarding the genotoxicity it was found that Bcl2 and survivineand caspase -3 as antiapoptotic genes were significantly down regulated and P53 as proapoptotic genes was significantly up regulated in both cell lines
ENZYMATIC KINETICS OF CELLULASES ISOLATED FROM SOIL BACTE RIA OF DOON VALLEY , UTTARAKHAND

Cellulases refers to a suite of enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze cellulolysis which is the hydrolysis of cellulose. Cellulose is the most abundant natural polymer on earth. It is the structural component of the plant cell walls which helps in the hydrolysis of 1, 4-beta-D-glycosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Cellulases are used for clarification of fruit juice, vegetable juice, roots, treatment of wine, extraction of oils and improving the quality of the bakery products. Eight soil samples were collected for cellulose preliminary screening from Gullarghati, Doon valley at different pH and temperatures, because maximum diversity was possible there as there was no interference by the humans. 110 colonies were isolated by the activity zone plate method containing CMC as a substrate using Congo red dye. Best twelve colonies were selected and checked using DNS method at 540 A0. Four strains BR-1, BR-2, BR-3 and BR-4 were used on the basis of spectrophotometerically and characterized with the study of substrate. Maximum velocity (Vmax) was observed for BR-2 i.e. 170 units per mg protein with Km of 49.50mg/ml. Strain BR-1 gave to pH optima at 4.5 and 6.5, strain BR-2 gave maximum activity at 4.5 and 7.0 pH, BR-3 strain gave maximum activity at pH 5.0 and 6. 5 with the highest yield of cellulases were obtained at pH 4.5, 5.5 and 7.0 in bacterial strain BR-4. The results also shows the effect of temperature bacterial strain BR-1, BR-2 and BR-4 with maximum cellulases activity at 450C and bacterial strain BR-3 maximum activity at 250C.
High-throughput live-imaging of embryos in microwell arrays using a modular, inexpensive specimen mounting system

Live-imaging embryos in a high-throughput manner is essential for shedding light on a wide range of questions in developmental biology, but it is difficult and costly to mount and image embryos in consistent conditions. Here, we present OMMAwell, a simple, reusable device that makes it easy to mount up to hundreds of embryos in arrays of agarose microwells with customizable dimensions and spacing. OMMAwell can be configured to mount specimens for upright or inverted microscopes, and includes a reservoir to hold live-imaging medium to maintain constant moisture and osmolarity of specimens during time-lapse imaging. All device components can be cut from a sheet of acrylic using a laser cutter. Even a novice user will be able to cut the pieces and assemble the device in less than an hour. At the time of writing, the total materials cost is less than five US dollars. We include all device design files in a commonly used format, as well as complete instructions for its fabrication and use. We demonstrate a detailed workflow for designing a custom mold and employing it to simultaneously live-image dozens of embryos at a time for more than five days, using embryos of the cricket Gryllus bimaculatus as an example. Further, we include descriptions, schematics, and design files for molds that can be used with 14 additional vertebrate and invertebrate species, including most major traditional laboratory models and a number of emerging model systems. Molds have been user-tested for embryos including zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), coqui frog (Eleutherodactylus coqui), annelid worm (Capitella teleta), amphipod crustacean (Parhyale hawaiensis), red flour beetle (Tribolium castaneum), and three-banded panther worm (Hofstenia miamia), as well mouse organoids (Mus musculus). Finally, we provide instructions for researchers to customize OMMAwell inserts for embryos or tissues not described herein. Summary Statement This Techniques and Resources article describes an inexpensive, customizable device for mounting and live-imaging a wide range of tissues and species; complete design files and instructions for assembly are included.
Identificación de la ruta de degradación de hidrocarburos aromáticos por medio de iniciadores degenerados en microorganismos.

La biorremediacion de hidrocarburos representa actualmente un reto biotecnologico por la lentitud con el que este contaminante es eliminado del sitio de impacto, actualmente, se han reportado varios generos bacterianos capaces de degradar hidrocarburos aromaticos. En este trabajo realizamos un analisis bioinformatico para el diseno de oligonucleotidos degenerados, cuyo blanco son los genes de degradacion de naftaleno. Se construyo una base de datos con los genes reportados en GeneBank y Kegg, para cada una de las etapas de la ruta (nahAc, nahad, nahB, nahD, nahF), se seleccionaron al menos 5 generos bacterianos por cada gene, estas secuencias fueron alineadas, y a partir del consenso se disenaron los oligonucleotidos, considerando una longitud promedio de 20 nt y 5 bases degeneradas. Estos oligonucleotidos fueron probados en diversos aislados bacterianos que degradan hidrocarburos identificadas como Pseudomonas aeruginosa, Providencia sp, Providencia rettgeri y Enterobacter sp. En los resultados de los PCR´s que se realizaron no se obtuvo amplificacion de los genes, lo que demuestra que las cepas llevan a cabo una degradacion por medio de la activacion de otras enzimas, lo que sugiere el diseno de mas oligonucleotidos que involucren mas generos bacterianos.
Segmentation of Honey Buyers’ Behaviour by Conjoint Analysis

Abstract A marketing analysis of Czech consumers’ behaviour when buying honey is discussed from the viewpoint of price, origin, honey type, crystallized sugar, and organic quality aspect. The surveyed target groups of honey consumers, who are examined also with respect to their education level, are from Prague and the Central Bohemian Region. The original premise of this research was the hypothesis that, when buying honey, customers focus primarily on its price and type. This hypothesis was verified by conjoint analysis. The results have shown that consumers are interested primarily in the price and origin of honey. An important parameter for buying honey is its (non)crystallization. Although it does not affect objective quality parameters of honey, it affects the consumers’ subjective perception of honey quality during purchase. Two clusters of honey consumers emerged through cluster analysis: the first cluster focussing on the origin, type, and price/sugar crystallization of honey, and the second interested in the origin, price, and quality of organic honey.
Nutrient utilization and reproductive performance in broiler breeder hens

Experiments were conducted to evaluate the influences of initial body-weight at photostimulation, diet density or feeding level on nutrient utilization and reproductive performance of broiler breeder hens. Additionally, the first experiment used two strains of broiler breeder females to determine if performance was similar when fed the different diets. These fast and slow feathering hens utilized dietary nutrients in a similar manner with no differences in body composition; however, the slow feathering hens laid more eggs to 34 wk of age than the fast feathering hens. Females with greater body weight produced a greater number of eggs through 40 wk of age. Low-body weight hens experienced body gains but were delayed, inconsistent layers through 40 wk of age. Feeding high-density diets or slightly more of a medium-density diet did not encourage greater egg production. INDEX WORDS: Broiler breeder hens, body weight, density diets, fast and slow feathering, feeding level NUTRIENT UTILIZATION AND REPRODUCTIVE PERFORMANCE IN BROILER BREEDER HENS
Positive Regulation of Macromolecule Metabolic Process Belongs to the Main Mechanisms Crucial for Porcine Oocytes Maturation

Summary The mammalian oocytes maturation is the compound process that involves morphological and molecular changes. These modifications include storage of macromolecules, which are crucial for proteins biosynthesis during periimplantation stages of embryo development. This study was aimed to investigate the genes expression profile encoding macromolecules important for regulation of proper porcine oocytes maturation. The porcine oocytes were collected from large ovarian follicles and analyzed both before and after in vitro maturation (IVM). Additionally, to check the developmental competence status, brilliant crezyl blue test (BCB) was performed. The obtained cDNA was used for biotin labeling and fragmentation by AffymetrixGeneChip® WT Terminal Labeling and Hybridization (Affymetrix). The preliminary analysis of the scanned chips was performed using AffymetrixGeneAtlasTM Operating Software. The created CEL files were imported into downstream data analysis software. In results, we found expression of 419 different genes, 379 genes were down-regulated and 40 genes were up-regulated in relation to the oocyte transcriptome before in vitro procedure. We observed up-regulation of all genes involved in “positive regulation of macromolecule metabolic process” before IVM as compared to transcriptional profile analyzed after IVM. In conclusion, we suggested that genes encoding proteins involved in macromolecule metabolism are important for achieving of porcine oocytes maturational stage. Moreover, the “activity of macromolecules metabolism” is much more increased in immature oocytes.
Effect of milk and oral electrolyte solutions with and without bicarbonate on abomasal luminal pH and systemic acid-base status in calves

Problemstellung: Bei Kalbern wird nach Zufuhr von Diattranken mit Bikarbonat-Ionen eine besonders ausgepragte Alkalisierung der Labmageningesta erwartet. Nachfolgend konnten die an saure pH-Werte gebundene abomasale Verdauung sowie unspezifische Infektabwehr beeintrachtigt sein. Material und Methode: Bei acht klinisch gesunden Kalbern wurde operativ eine Plastkanule in den Labmagen eingesetzt. Danach erhielten die Tiere uber sieben bis neun Tage als Nahrung alternierend 1) Kuhmilch, 2) bikarbonatfreie oder 3) bikarbonathaltige Diattranke. Auserdem wurde 4) das Gemisch aus gleichen Teilen bikarbonathaltige Diattranke und Milch verabreicht. In den uber die Kanule entnommenen Labmageningesta bestimmten wir die Werte fur pH, Flache unter der pH-Wert-Kurve (AUC) und [SID3]. Weiterhin wurde vergleichend im arteriellen und venosen Blut der systemische Sauren-Basen-Status anhand traditioneller Henderson- Hasselbalch-Parameter sowie der Stewart-Variablen ermittelt. Ergebnisse: Die Futterung von Milch bewirkte bei den Kalbern einen Anstieg des Labmagen-pH von Nuchternbefunden mit 2,00 ± 0,44 auf Werte bis 4,70 ± 0,41 uber zwei Stunden. Die AUC-Werte bis vier Stunden postprandial betrugen 898 ± 87 (= 100%). Die in Milch zubereitete bikarbonatfreie Diattranke fuhrte zur signifikant basischeren Auslenkung des abomasalen pH mit Werten bis 5,35 ± 0,31 sowie AUC = 1084 ± 89 (= 121%). Die mit Wasser hergestellte bikarbonathaltige Diattranke allein und ebenso ihr Gemisch mit Milch verursachten den transient starksten Anstieg des Labmagen-pH fur 1,5 bzw. 0,5 Stunden auf Werte bis 6,59 ± 0,28 bzw. 6,22 ± 0,12. Die AUCWerte unterschieden sich mit 1119 ± 45 (= 125%) und 1126 ± 44 (= 125%) signifikant von den Befunden nach Milchtranke, jedoch nicht von den Resultaten nach Gabe der bikarbonatfreien Diattranke. Systemisch bewirkten die Futterungen zum Zeitpunkt zwei Stunden postprandial eine im arteriellen und venosen Blut gleichermasen nachweisbare geringe, teilweise signifikante basische Reaktion, wie ↑ pH, ↑ [HCO3 –], ↑ [BE], ↑ [SID3] und ↓ [Atot] bei unveranderten Werten fur PCO2. Die postprandial im Blut der Kalber festgestellte „basische Flut“ war nach Gabe der bikarbonathaltigen Diattranken relativ am deutlichsten ausgepragt. Schlussfolgerung: Im Vergleich zur ublichen Milchfutterung verursachte die in Milch zubereitete bikarbonatfreie Diattranke postprandial signifikant starkere basische Auslenkungen des Labmagen-pH. Mit Wasser hergestellte bikarbonathaltige Elektrolyttranken fuhrten kurzfristig (≤ 2 h) zu noch starkerem Anstieg des Labmagen-pH. Die AUC der pH-Wert-Kurve bis vier Stunden postprandial (= zeitabhangige „Wirksamkeit“) differierte jedoch nicht signifikant von der nach Gabe der bikarbonatfreien Diattranken.
Effects of carotenoid sequestration on a caterpillar's cryptic coloration and susceptibility to predation

Carotenoids are used for many functions by animals, including combining with other pigments to produce aposematic and cryptic coloration. Carotenoids in combination with blue pigments are responsible for green coloration in many caterpillars, and thus carotenoid sequestration may reduce their contrast against a green foliage background. We tested the hypothesis that carotenoid sequestration reduces contrast and enhances survival by rearing Trichoplusia ni Hübner (Lepidoptera: Noctuidae) on Brassica oleracea L. var. Acephala (Brassicaceae) leaves and exposing them to predators. We found that carotenoids derived from the host plant are partially excreted, along with chlorophyll, but also sequestered in hemolymph. Larvae that were given plants that provided carotenoids showed less contrast against their host plants within 1 day compared to larvae that were not provided with carotenoids. Last, both short‐term field observations and laboratory trials of larvae caged with predatory Podisus maculiventris Say (Hemiptera: Pentatomidae) nymphs showed that survival of carotenoid‐sequestering larvae was higher compared to larvae that did not sequester. These results suggest that carotenoid sequestration may be an important adaptive strategy that reduces susceptibility to natural enemies that hunt by sight. Further research that examines the mechanisms by which carotenoids are absorbed and modified will lend insights into the evolution of carotenoids functioning as passive defensive compounds.
Pse-in-One 2.0: An Improved Package of Web Servers for Generating Various Modes of Pseudo Components of DNA, RNA, and Protein Sequences

Pse-in-One 2.0 is a package of web-servers evolved from Pse-in-One (Liu, B., Liu, F., Wang, X., Chen, J. Fang, L. & Chou, K.C. Nucleic Acids Research, 2015, 43:W65-W71). In order to make it more flexible and comprehensive as suggested by many users, the updated package has incorporated 23 new pseudo component modes as well as a series of new feature analysis approaches. It is available at http://bioinformatics.hitsz. edu.cn/Pse-in-One2.0/. Moreover, to maximize the convenience of users, provided is also the stand-alone version called “Pse-in-One-Analysis”, by which users can significantly speed up the analysis of massive sequences.
Assessing the scope for genetic rescue of an endangered butterfly: the case of the Eltham copper

Genetic rescue is an under‐utilised conservation strategy used to boost the genetic diversity and/or fitness of small, isolated populations through the introduction of novel genes. Effective implementation of genetic rescue requires an understanding of the evolutionary history and genetic distinctiveness of populations. The Eltham copper butterfly (ECB) is an endangered subspecies that exists as small, isolated populations across four disjunct regions in Victoria, Australia. Mitochondrial and nuclear sequence data were used to assess the genetic distinctiveness of ECB from its nearest relative: the fiery dull copper butterfly (FDC), explore the evolutionary history and population structure of ECB across its contemporary distribution, and assess the scope for genetic rescue of the most‐threatened ECB population in Eltham‐Greensborough. Findings support the current status of ECB and FDC as distinct evolutionary units, which should continue to be managed separately given current knowledge. Modest population genetic structure across the range of ECB was detected. However, low levels of historical gene flow and shared haplotypes between Eltham‐Greensborough and the northern regions suggest relatively recent divergence. Given relatively recent divergence, low population numbers and low genetic diversity, the population located in the Eltham‐Greensborough region is a strong candidate for genetic rescue. Using established criteria, explicit recommendations are made for the implementation of genetic rescue via translocations. Genetic rescue, together with ongoing habitat management, should improve genetic diversity, fitness and persistence of the ECB in the region most threatened by urban disturbance. Any risks associated with genetic rescue in conservation should be weighed against extinction risk as a result of inaction.