Miracle-dz/UniFAR-FTUs huggingface dataset:
ANTIBACTERIAL ACTIVITY OF LEAF AND SEED EXTRACTS OF DELONIX REGIA AND ACHYRANTHUS ASPERA AGAINST SELECTED BACTERIAL STRAINS

The antibacterial activity of petroleum ether, chloroform and ethanol extracts of the leaf and seed of Delonix regia and Achyranthus aspera were evaluated using agar well diffusion method against five bacterial strains namely, Bacillus subtilis, Escherichia coli, Enterobacter aerogenes, Micrococcus luteus, Pseudomonas aeruginosa. Chloramphenicol was used as standard. Among the three solvents analysed in leaf and seed, chloroform seed extract of D. regia and ethanol seed extract of A. aspera exhibited a high inhibitory zone against E. coli than other bacterial strains. Hence the phytoconstituents present may be used as antibiotic drugs.
The rhizosphere : biochemistry and organic substances at the soil-plant interface

Rhizosphere as a site of biochemical interactions among soil, plant and microorganisms type and amounts of compounds released by plants in the rhizosphere the release of exudates as affected by the physiological status of plants (water, physical and nutritional stress) influence of root exudates on the rhizosphere microbial populations direct vs. indirect effects of soil humic substances on plant growth and nutrition mineralization of organic compounds in the rhizosphere organic signals between plants and microorganisms microbial siderophores biochemistry of the association between mycorrhizas and plants biochemistry of the interaction between rhizobia and the host plant modelling processes in the rhizosphere methodological approaches to the study of the rhizosphere.
La barrière de diffusion, une nouvelle fenêtre pour l’exclusion

Partenariat médecine/sciences Écoles doctorales (3) L’actualité scientifique vue par les étudiants du Master Biologie Santé, module physiopathologie de la signalisation, Université Paris-Saclay > Nous poursuivons dans ce numéro la publication des Nouvelles rédigées par les étudiants du Master « Biologie Santé », dans le cadre du module « physiopathologie de la signalisation » de l’université Paris-Saclay. Ces textes s’inscrivent dans le développement d’un partenariat que médecine/ sciences propose aux Écoles doctorales (voir à ce propos l’Éditorial de Hervé Chneiweiss, m/s n° 6-7, juin-juillet 2016, page 537). Après les quatre Nouvelles publiées dans le numéro de juinjuillet 2016, précédées d’une introduction des enseignants participants, et les cinq Nouvelles publiées dans le numéro d’août-septembre 2016, voici une troisième série de cinq Nouvelles. Toutes ces Nouvelles sont en accès libre sur le site de m/s (www.medecine/ sciences.org). Bonne lecture ! < Karim Benihoud (professeur, université Paris-Sud) Sophie Dupré (maître de conférences, université Paris-Sud) Olivier Guittet (maître de conférences, université Paris-Sud) Boris Julien (maître de conférences, université Paris-Sud) Hervé Le Stunff (professeur, université Paris-Sud) Philippe Robin (maître de conférences, université Paris-Sud) karim.benihoud@u-psud.fr
Identification of DNA sequence variants in the estrogen receptor pathway in breast cancer

Breast cancer is of public health importance with an increasing incidence over the past decade. Estrogen Receptor (ER) activity is critical for promoting majority of breast cancers. Inhibiting ER is one of the most successful targeted therapies in oncology. Studies have suggested that genomic variation in ER binding sites and ESR1 gene may be responsible for endocrine treatment response and cancer progression. We investigated the role of single nucleotide variants (SNVs) in the ER pathway in breast cancer, including clinically relevant mutations in ER gene and regulatory variants in ER binding sites. First, we developed a computational pipeline to identify SNVs in ER binding sites, using chromatin immunoprecipitation-sequencing (ChIP-seq) data from hormone responsive breast cancer cells and tumors. Analysis of ER ChIP-seq data from multiple MCF7 studies characterized a SNV within intron 2 of the IGF1R gene, rs62022087, predicted to increase the affinity for ER binding. By integrating 43 ER ChIP-seq data sets, multi-omics and clinical data, we identified SNVs regulating downstream target genes which may contribute to patients’ survival. Second, we used sensitive detection methods to detect mutations and identified high frequencies ESR1 mutations in primary tumors, metastatic lesions and cell-free DNA samples. This result may be due to higher sensitivity of our study in detecting mutations at very low allele frequency. Finally, we generated appropriate knock-in cell lines through CRISPR technology to study ER mutations. RNA-seq studies revealed ER mutations are can activate estrogen regulated genes in a ligand independent manner and also may induce/repress a set of novel targets. Cell adhesion assays demonstrated mutants are less adhesive to Collagen I which may be a marker of metastasis. Taken together, our findings indicate that SNVs in ER pathway are clinically important and may predict drug response in ER+ breast cancer. From the public health perspective, screening for these impactful variants will be soon part of the genetic testing as our knowledge of genome improves. This will eventually help initiatives to reduce public health burden by choosing the right treatment for breast cancer patients in personalized manner.
Identification of Genetic and Expression Markers in DLBCL Cell Lines That Influence the In Vivo Response of DLBCL to Doxorubicin.

Diffuse large B-cell lymphoma (DLBCL) is the largest aggressive group of non-Hodgkin’s lymphoma (~40%) and exhibits great clinical and pathological heterogeneity. While DLBCL represents a chemosensitive disease, ultimately, only approximately 50% of patients are cured with current treatment options. Standard front-line therapy comprises CHOP and more recently Rituximab-CHOP. CHOP commonly contains doxorubicin as the curative anthracycline. Controversy currently exists in the use of genetic and expression markers in predicting response to treatment and outcome of DLBCL, thus, we examined the cellular responses of a panel of eight DLBCL cell lines to doxorubicin in order to define molecular markers that influence the response. Expression profiling and subsequent classification of the cell lines revealed that six of the lines were of a germinal center B-cell-like (GCBL) subtype and two (Ly3 and Ly10) were of a non-GCBL subtype. Ly3 and Ly10 exhibited a rapid apoptotic response within 24 hours after exposure to doxorubicin as evaluated by Hoescht staining. Expression profiling of the response of Ly10 cells (in triplicate) revealed the up-regulation of transcripts consistent with mediation of the cellular response via a p53-dependent pathway. Mutation analysis and Western blotting revealed wild type TP53 in Ly3 and Ly10 with an induction of p53 levels after doxorubicin. The remaining cell lines exhibited mutated TP53 sequences and no induction of p53 by doxorubicin. Therefore, in DLBCL cell lines, wild type p53 effects an early rapid apoptotic response to doxorubicin. In the six non-GCBL cell lines, a decrease in viability after doxorubicin was observed at much later times (up to 48 hours after treatment) by both apoptotic (exemplified by Ly2 and Ly8) and non-apoptotic mechanisms (exemplified by Ly1). Expression profiling of these three cell lines revealed alterations in expression of transcripts consistent with a G2/M cell cycle delay induced by doxorubicin, which was confirmed by follow-up flow cytometric analysis. An induction of transcripts consistent with NF-κB and AP-1 activation was observed in Ly1, but not in Ly2 and Ly8, which was confirmed by electrophoretic mobility shift assays. In order to determine if this cellular response plays a role in determining the response of DLBCL to doxorubicin in vivo, the expression profiles of untreated Ly1 and Ly2 were compared, and the resulting 160 differentially expressed transcripts were used to cluster 41 newly-diagnosed DLBCL specimens which had previously been profiled and had a known response to doxorubicin-containing therapy. This analysis revealed a marked correlation between capacity to induce NF-κB and AP-1 with in vivo treatment failure. Overall, these experimental studies have begun to outline genetic and biologic features that together contribute to the response of DLBCL to doxorubicin in vivo.
A false‐positive food chain error associated with a generic predator gut content ELISA

Conventional prey‐specific gut content ELISA (enzyme‐linked immunosorbent assay) and PCR (polymerase chain reaction) assays are useful for identifying predators of insect pests in nature. However, these assays are prone to yielding certain types of food chain errors. For instance, it is possible that prey remains can pass through the food chain as the result of a secondary predator (hyperpredator) consuming a primary predator that had previously consumed the pest. If so, the pest‐specific assay will falsely identify the secondary predator as the organism providing the biological control services to the ecosystem. Recently, a generic gut content ELISA was designed to detect protein‐marked prey remains. That assay proved to be less costly, more versatile, and more reliable at detecting primary predation events than a prey‐specific PCR assay. This study examines the chances of obtaining a ‘false positive’ food chain error with the generic ELISA. Data revealed that the ELISA was 100% accurate at detecting protein‐marked Lygus hesperus Knight (Hemiptera: Miridae) remains in the guts of two (true) primary predators, Hippodamia convergens Guérin‐Méneville (Coleoptera: Coccinellidae) and Collops vittatus (Say) (Coleoptera: Melyridae). However, there was also a high frequency (70%) false positives associated with hyperpredators, Zelus renardii Kolenati (Hemiptera: Reduviidae), that consumed a primary predator that possessed protein‐marked L. hesperus in its gut. These findings serve to alert researchers that the generic ELISA, like the PCR assay, is susceptible to food chain errors.
Crambe meal in diets supplemented with enzyme complex solid state fermentation (SSF) for Nile tilapia

Nile tilapia performance fed with diets containing crambe meal supplied with enzyme complex SSF was evaluated. With initial average weight ranging between 1.133g ± 0.105, 280 Nile tilapias were randomized into seven treatments, with four replicates and 10 fish per tank, totaling 28 experimental units. The temperature-controlled recirculation system had 30 L per tank, with individual water supply and aeration. The physico-chemical parameters of the water (temperature, dissolved oxygen, ammonia and pH) were monitored periodically. The fish went through an adaptation period of one week prior to starting the trial. The treatments consisted of a control diet and others diets containing three levels of inclusion of crambe meal, being replaced in their proper proportion, the protein soya by the protein ingredient evaluated (5, 10 and 20%) with 500 ppm of enzyme complex SSF or not. The isoproteic diets (360 g.kg-1) contained the same amount of the ingredients, changing only the levels of inclusion of soya meal, crambe meal and inert. Fish were fed ad libitum four times per day. At 56 days, the tilapia performance was evaluated. The physic and chemistry parameters of water were within of the levels recommended for the species during all experimental time There was statistical difference for final weight, weight gain and feed conversion. It is concluded that the inclusion of up to 10% crambe meal supplemented with 500 ppm of enzyme complex SSF provides better performance and higher nitrogen retention for Nile tilapia. Key words: Additives, Crambe abyssinica, fish nutrition, fish performance, Oreochromis niloticus.
Rozpoznawanie antygenów prątków przez fagocyty* Recognition of mycobacterial antigens by phagocytes

Rozpoznawanie antygenow prątkow przez receptory fagocytow jest nie tylko glownym elementem pierwszej linii obrony, ale rowniez waznym lącznikiem mechanizmow obronnych naturalnych i swoistych adaptacyjnych. Odpowiedź odpornościowa funkcjonuje w oparciu o istnienie określonej liczby receptorow PRR (pattern recognition receptors), rozpoznających konserwatywne struktury drobnoustrojow zwane PAMP (pathogen associated molecular patterns). Receptory te biorą udzial w procesach opsonizacji i fagocytozy patogenow, aktywacji ukladu komplementu, indukcji procesu apoptozy oraz w uruchamianiu systemow przekazywania sygnalow komorkowych. Zainicjowana kaskada przenoszenia sygnalu ma mobilizowac sily obronne organizmu do walki z wnikającym patogenem i ma na celu jego szybką eliminacje z ustroju. Zrozumienie roli tych receptorow w przeciwprątkowej odpowiedzi immunologicznej wydaje sie w pelni uzasadnione ze wzgledu na mozliwośc wykorzystania uzyskiwanej wiedzy w typowaniu osob o zwiekszonej podatności na gruźlice, konstruowaniu szczepionek nowej generacji dla celow profilaktycznych i terapeutycznych oraz nowych biomarkerow usprawniających ciągle trudną i czasochlonną diagnostyke mikobakteryjnych zakazen.
Anti-obesity effect of Solidago virgaaurea extract in high-fat diet-fed SD rat

ABSTRACT In our previous report, Solidago virgaurea var. gigantea (SV) extract was shown to exhibit anti-adipogenesis activity in 3T3-L1 adipocyte cells. In this study, anti-obesity activity of SV extract was investigated in in vivo animal model. Sprague-Dawley (SD) rats were administered with high-fat diet, and the effect of SV extract was tested. SD rats were treated orally with SV extract for eight weeks, and their body weight was measured every week. The oral treatment of SV extract decreased body weight, fat tissue weight, blood low-density lipoprotein-cholesterol level, and blood triglycerides level. The p-AMP-activated protein kinase (AMPK) (AMP kinase) protein level in the fat tissue of the SV extract-treated SD rats increased. The protein levels of AMPK-downstream proteins, c-AMP response element binding protein and acetyl-CoA carboxylase, fatty acid synthase, and FABP4 decreased, indicating that SV extract-activated AMPK induced inhibition of adipogenesis and lipid biosynthesis in fat tissue. 1H-NMR measurements of the lipid soluble liver extract showed a decrease in the lipid metabolites, indicating that SV extract-activated fatty acid oxidation in the liver. Overall, our results suggest that orally treated SV extract has excellent anti-obesity effect against HFD-induced obesity of SD rat.
Agglutinazione Cromosomica (”Stickiness„) Quale Causa di Eccezionali Condizioni Nucleari Nelle Cellule del Tappeto di Crepis Zacintha (L.) Babc.

RIASSUNTOL'A. studia l'evoluzione delle cellule del tappeto in Crepis Zacintha (L.) Babc.Queste cellule inizialmente mononucleate subiscono nel loro sviluppo tre divisioni successive e quindi degenerano senza produrre un periplasmodio.La condizione definitiva sarebbe, al termine della 3a divisione, tipicamente 8 nucleata, se l'insorgere di fenomeni di agglutinazione cromosomica durante la 2a e 3a divisione non modificassero piu o meno profondamente il risultato finale. Sono stati osservati i seguenti fenomeni di agglutinazione: a) ponti anafasici persistenti anche dopo raggiunto lo stadio quiescente (fenomeno definito « agglutinazione anafasica permanente »);b) ponti anafasici dissolti prima della reversione telofasica (« agglutinazione anafasica temporanea »);c) agglutinazione telofasica tra gruppi cromosomici appartenenti a fusi diversi (« agglutinazione telofasica interfusale »);I fenomeni a), b), c) sono assenti durante la 1a divisione, sono rari durante la 2a e frequenti durante la 3a.La 1a divisione.
Alıç (Crataegus orientalis) meyvesinin antioksidan aktivitesi ve fenolik bileşiklerinin ekstraksiyonu üzerine farklı çözgenlerin etkisi

Bitkisel materyallerden biyoaktif bilesiklerin ekstraksiyonu besinsel destek uretimi ve endustriyel atiklardan bilesiklerin geri kazanimi gibi proseslerin en onemli asamalarindan biridir. Ekstraksiyon, solvent cesidi, partikul boyutu, ekstraksiyon suresi ve sicakligi gibi faktorlerden etkilenmektedir. Bu arastirmada farkli cozgenlerle ekstrakte edilen alic (Crataegus orientalis) meyvesinin toplam fenolik madde iceriginin, antioksidan aktivitesinin ve fenolik madde profilinin belirlenmesi ve en uygun cozgenin tespiti amaclanmistir. Beysehir’de dogal olarak yetisen agaclardan toplanan alic meyveleri su, metanol ve metanol:su (1:1) karisimi ile ekstrakte edilmistir. En yuksek antioksidan aktivite ve toplam fenolik icerigi metanol:su ekstraktinda elde edilmistir. Prosiyanidin B1 ve B2, (-)-epikatesin, epigallokatesin gallat ve rutin ekstraksiyonunda en iyi cozucunun metanol:su karisimi oldugu, gallik asidin suda daha iyi ekstrakte edildigi tespit edilmistir.
Immunological responses and mechanisms of action of the TLR2-ligand Neisserial PorB vaccine adjuvant

viii TABLE OF CONTENTS . x LIST OF FIGURES . xiii LIST OF ABBREVIATIONS . xvii CHAPTER ONE: INTRODUCTION . 1 Vaccines . 1 History and Successes . 1 The Need for New and Improved Vaccines . 3 Adjuvants . 4 Definition and History . 4 Pattern Recognition Receptors (PRRs) . 6 TLR-ligand Based Adjuvants . 11 Specific Aims and Hypothesis . 16 CHAPTER TWO: MATERIALS AND METHODS . 20 Methods for Chapter Three: . 20 Methods for Chapter Four: . 40 Methods for Appendix . 46 xi CHAPTER THREE . 49 Intact MyD88 Signaling in Macrophages is Required for Antibody and Germinal Center Induction by TLR-Ligand Based Adjuvants. 49 Abstract . 49 Introduction . 50 Results . 54 Discussion . 82 CHAPTER FOUR . 93 Induction of Robust and Diverse T Cell Responses by TLR2 Ligand Based Adjuvant, Meningococcal PorB. 93 Abstract . 93 Introduction . 94 Results . 99 Discussion . 117 Conclusion . 125 Summary of Results . 125 Future Directions . 126 Significance . 130 APPENDIX . 133 A1. Lack of MyD88 in macrophages increased anti-inflammatory cytokine IL-10 upon immunization with TLR-ligand based adjuvant. 133 A2. Humoral responses two weeks after the 1 and 2 immunizations. 134 xii A3. Humoral response induced by MF-59 is MyD88 dependent. 136 A4. Tissue sectioning and staining for germinal centers and CD169 macrophages. 137 A5. Germinal center formation in lymph nodes of WT mice compared to Mac-MyD88/mice. 142 A6. CD169 macrophage staining in WT compared to Mac-MyD88-/mice. 144 A7. Germinal center formation in spleen of WT mice compared to DC-MyD88-/mice. 145 A8. BAFF and IL-21 cytokines level in WT vs Mac-MyD88-/upon immunization. 146 A9. TLR2-ligand based adjuvant PorB increase the number of antigen positive DCs in the draining lymph nodes of WT mice. 150 A10. In vivo and in vitro microarray analysis for further understanding of PorB’s adjuvant activity. 153 BIBLIOGRAPHY . 160 CURRICULUM VITAE . 189
Genetic analysis of palmitic acid contents using two soybean mutants, J3 and J10

Development of soybean [Glycine max (L.) Merr. ] varieties with altered palmitic acid content increase the utility of the oil for different edible purposes. The palmitic acid content in the seed oil of common soybean varieties is about 11.0 %. Sovbean mutants with reduced and elevated palmitic acid have been developed. The objective of this study was to determine the relationships between the genetic systems controlling palmitic acid content in these mutants. Reciprocal crosses were made between each mutant and its original variety, Bay and between the two mutants. No maternall and cytoplasmic effects were found in these crosses. There was no dominance for palmitic acid content in J3×Bay and J3×J10 crosses, while in J10×Bay cross, a partial dominant effect was observed. Analysis of F2 seeds from F1 plants in both of J3×Bay and J10×Bay crosses showed three distinct peaks for palmitic acid content which satisfactorily fit a 1 : 2 : 1 ratio.
Wild Pollinators Enhance Fruit Set of Crops Regardless of Honey Bee Abundance

Honeybees Can't Do It Alone The majority of food crops require pollination to set fruit with the honeybee providing a pollination workhorse, with both feral and managed populations an integral component of crop management (see the Perspective by Tylianakis, published online 28 February). Garibaldi et al. (p. 1608, published online 28 February) now show that wild pollinators are also a vital part of our crop systems. In more than 40 important crops grown worldwide, wild pollinators improved pollination efficiency, increasing fruit set by twice that facilitated by honeybees. Burkle et al. (p. 1611, published online 28 February) took advantage of one of the most thorough and oldest data sets available on plant-pollinator interaction networks and recollected data on plant-pollinator interactions after more than 120 years of climate change and landscape alteration. The historical data set consists of observations collected by Charles Robertson near Carlinville, Illinois (USA), in the late 1800s on the phenology of plants and their pollinating insects, as well as information about which plants and pollinators interacted with one another. Many sites were revisited in the early 1970s and in 2009 and 2010 to collect similar plant-pollinator data. Pollinator function has declined through time, with bees showing lower visitation rates and lower fidelity to individual plant species. Flower visits by wild insects enhanced fruit production in crops worldwide, well beyond the effect of bees. [Also see Perspective by Tylianakis] The diversity and abundance of wild insect pollinators have declined in many agricultural landscapes. Whether such declines reduce crop yields, or are mitigated by managed pollinators such as honey bees, is unclear. We found universally positive associations of fruit set with flower visitation by wild insects in 41 crop systems worldwide. In contrast, fruit set increased significantly with flower visitation by honey bees in only 14% of the systems surveyed. Overall, wild insects pollinated crops more effectively; an increase in wild insect visitation enhanced fruit set by twice as much as an equivalent increase in honey bee visitation. Visitation by wild insects and honey bees promoted fruit set independently, so pollination by managed honey bees supplemented, rather than substituted for, pollination by wild insects. Our results suggest that new practices for integrated management of both honey bees and diverse wild insect assemblages will enhance global crop yields.