Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and screening of pyocyanin producing Pseudomonas spp. from soil

Pseudomonas spp. produces large quantities of water soluble blue green phenazine pigment pyocyanin. The blue green chloroform soluble phenazine pigment extracted from Pseudomonas spp has antimicrobial activity. In present study a total of nine bacterial isolated screened from the different environment sample. The isolates obtained were gram negative, non-spore forming and exhibited fluorescence under UV light. The isolate showing blue green pigment on king’s B agar medium at a temperature of 35oC after 48-72 hr. of incubation and considered as having capabilities to produce pyocyanin.
PO-235 Integrin beta-like 1 overexpression stimulates invasiveness of ovarian cancer cells in vitro

Introduction In our previous microarray study we analysed gene expression profile of over 100 ovarian cancer samples.1 We identified two molecular subgroups of high grade serous ovarian cancers (HG-SOC) with distinct gene expression profiles and survival.2 Among differentially expressed genes was an Integrin beta-like1 gene (ITGBL1). ITGBL1 is a poorly characterised protein, structurally cognate with integrin β. Our aim was to study whether and how ITGBL1 can influence the phenotype of ovarian cancer cells. Material and methods ITGBL1 coding sequence was PCR-amplified from cDNA and cloned into pLNCX2 vector. Retroviral system was used to obtain two ovarian cancer cell lines: OAW42/ITGBL1(+) and SKOV3/ITGBL1(+) with overexpression of ITGBL1. Control cell lines were obtained by transduction with empty vector. A Matrigel cell invasion assay was performed using 24-well transwell inserts (coated with fibronectin and matrigel). Crystal violet staining of invaded cells was performed, then the dye was solubilized with 10% acetic acid and the absorbance was measured at a wavelength of 595 nm. Results and discussions We compared invasion rate of control OAW42 and SKOV3 cells with that of isogenic cell lines containing ITGBL1 construct. The results indicate that ITGBL1 overexpression increases invasiveness of ovarian cancer cells. Conclusion Our results indicate that ITGBL1 may increase ovarian cancer cell invasion rate. Along with our previous reported results that overexpression of ITGBL1 may increase migration, decrease adhesion3 and has no effect on proliferation rate,4 this results suggests that ITGBL1 may play an important role in ovarian cancer progression enabling easier spreading of the cells within peritoneal cavity. References KM Lisowska, et al. Front. Oncol2014. doi:10.3389/fonc.2014. 00006 KM Lisowska,et al. J. Cancer Res. Clin. Oncol2016. doi:10.1007/s00432-016-2147-y AJ Cortez, et al. Int. J. Gynecol. Cancer2016; 26(3):665. AJ Cortez, et al. Int. J. Gynecol. Cancer2017;27(4):1931.
ASCITES VERSUS SUDDEN DEATH SYNDROME (SDS) IN BROILER CHICKENS: A REVIEW

The demand for meat is increasing continuously in developing countries. Therefore, the modern broiler chickens have been intensely selected for higher growth rate, increased feed conversion, and meat yield. However, Ascites and Sudden Death Syndrome (SDS) poses a serious challenge to the poultry industry and had caused a great economic loss worldwide. Ascites syndrome which is also called pulmonary hypertension syndrome (PHS) refers to the fluid accumulation in the abdominal cavity which develops gradually and is often triggered by inadequate oxygen levels. Sudden death syndrome (SDS) on the other hand is non infectious and often characterized by sudden death of a healthy and heavy bird without discernible cause. It usually occurs suddenly within few seconds; the affected birds flip over on their backs and die. This review is meant to highlight the differences between these two metabolic disorders to enable poultry farmers evaluate the probable causes of mortalities in their flock.
Olfaction as a Cue for Nest-Site Choice in Turtles

Abstract Nest-site choice in turtles has a demonstrated impact on their fitness. Previous studies of nest-site choice have focused on environmental factors potentially affecting that choice (e.g., temperature, insolation, soil type, or moisture). Observations of nesting of painted turtles (Chrysemys picta) at the Crescent Lake National Wildlife Refuge in the Nebraska Sandhills suggest that females might use olfactory cues (specifically odors of other nesting females) to choose nest sites. We tested this hypothesis indirectly by using the nearest neighbor (nest) distance algorithm in ArcMap 10.1. Our results for nests in 2012–2014 were mixed, with nesting at some sites, in some years, and by some turtles occurring nonrandomly, in very close proximity to previous nests. Preliminary experimental data from 2015 using urine-treated sites in primary nesting areas also suggested that females showed more interest in those sites than sites moistened with equal amounts of water. These data provide some support for the use of nest odor as an important cue for nest-site choice in turtles, but they are insufficient to reject the possibility of the simultaneous use of other fine-scale environmental cues.
Structural Basis of Hoogsteen Base Pair Recognition by the DNA-Binding Domain of the Transcription Factor p53

p53 is a tumor suppressor protein activated during DNA damage and cell stress that plays a central role in apoptosis, cell cycle arrest, DNA repair, and senescence. In human, 50% of cancer cases have a mutation in p53. Approximately, 85% of these mutation cases occur within the DNA-binding domain (DBD) of p53, which is known to interfere with its ability to bind to the p53 response elements (p53REs). Many structures of the p53DBD in complex with DNA have been previously solved. However, how p53DBD recognizes DNA is not fully understood. In this work, I address how p53DBD recognizes the center of its half-site response elements. First, I investigated the specificity of p53DBD to the central base pair of the half -site REs by fluorescence anisotropy. The results show that p53DBD favors adenine and thymine over cytosine and guanine. Furthermore, I obtained high-resolution crystal structures of p53DBD bound as a dimer to its half-sites. Theses structures show a Hoogsteen conformation at the central A-T, A-A and T-T doublets of DNA sequences. Moreover, in all of the obtained structures, the Arg248 residue from each p53DBD monomer contacts the central base pairs by water-mediated hydrogen bonds through the DNA minor groove. These findings indicate the significance of Hoogsteen base pairs conformation to the function of p53 as a transcription factor. Furthermore, it reveals the importance of Arg248 residues in p53 recognition to its activating REs
Formes soluble et membranaire de la choline acétyltransférase chez la mouche "Drosophila melanogaster"

La choline acethyltransferase (ChAT) catalyse la biosynthese du neurotransmetteur acetylcholine. Outre sa forme soluble, hydrophile, nous avons demontre l'existence d'une forme membranaire, amphiphile, de la ChAT dans la tete de Drosophile. Les taux d'enzyme membranaire augmentent au cours du developpement. Nous avons clone un ADNc complet (4.2 kb) codant pour la ChAT de Drosophile. Les ovocytes de Xenope injectes expriment une activite amphiphile. L'activite amphiphile n'est pas enrichie dans les membranes. La ChAT amphiphile native et recombinante sont moins sensibles a l'inhibition par l'acetylcholine ainsi qu'a la denaturation thermique. Des fibroblastes et des neuroblastomes transfectes de facon stable expriment une activite amphiphile. Il semble que la ChAT amphiphile ne soit enrichie que dans les membranes de cellules d'origine nerveuse. Nous avons produit un anticorps contre une proteine de fusion couvrant la partie C-terminale de la ChAT. Cet anticorps reconnait la proteine precurseur de l'enzyme de Drosophile a 75 kDa.
Screening for the expression of soluble recombinant protein in E. coli

Author(s): Doyle, Sharon A. | Abstract: Protein expression and purification have traditionally been time-consuming, case-specific endeavors, and are considered to be the greatest bottlenecks in most proteomics pipelines. Eschericia coli (E. coli) is the most convenient and cost-effective host, although optimal conditions for the expression of different proteins vary widely. Proteins vary in their structural stability, solubility and toxicity in this environment, resulting in differing rates of protein degradation, formation into insoluble inclusion bodies and cell death, thus affecting the amount of soluble protein that can be obtained from E. coli grown in culture. A variety of E. coli strains designed to address many of these problems have been made, by allowing for disulfide bond formation in the E. coli cytoplasm, more efficient usage of codons that are rarely found in E. coli genes, and a reduction of specific E. coli proteases. The T7 expression system has also helped to alleviate many problems associated with recombinant expression by allowing for tightly regulated induction of expression. However variability in the recombinant expression of proteins still exists. Induction strength and time, and growth temperature are just a few parameters that can have drastic effects on the amount of soluble protein that can be obtained from the E. coli host. Adding further complexity to this problem, affinity tags that are used as a means to standardize protein purification have varying effects on protein stability and solubility. The hexahistidine tag, which allows for protein to be adsorbed to Ni2+-charged resin, is often used because it is small and often does not need to be removed by protease digestion prior to downstream experimentation. Another useful tag is the maltose binding protein (MBP) tag, which allows for the protein to be captured with amylose resin, and can stabilize and solubilize the fusion partner. A variety of affinity tags, in addition to their placement at the N- or C- terminal end of the coding sequence, needs to be tested for optimal protein expression. To take full advantage of the variety of strategies developed to improve the expression of soluble protein in E. coli, a means to test easily and rapidly many growth parameters is necessary. This chapter describes a dot-blot expression screen to test the effects of growth and induction parameters on the yield of soluble protein. The expression screen is used to detect hexahistidine-tagged proteins expressed in E. coli, however it is adaptable for the detection of other affinity tags or fusion partners that have suitable antibodies available. In this example, induction time and temperature are tested, however, it can be used to test additional parameters such as affinity tag type and placement, E. coli host type, and growth medium formulations. Results of the screen may be used to segregate samples into groups for further parallel processing in an efficient high-throughput protein production pipeline.
Sex and Age-Specific Variation In Provisioning By A Long Distance Neotropical Migrant, the Wood Thrush (Hylocichla mustelina)

ABSTRACT Parental investment is a unique balance between optimizing reproductive success and survival, yet how individuals vary their effort with respect to age and the contributions of their partner remains poorly studied. Here, we examine the provisioning of nestlings by Wood Thrushes (Hylocichla mustelina) at 38 nests in southern Indiana during the breeding season of 2013 to address the influence of adult age and sex on reproductive investment. We used video cameras to quantify an adjusted provisioning rate (provisioning rate = adult visits/hr/nestling × mean prey size × mean number of prey/visit) by individuals in both age-assortative (same age) and disassortative (different age) pairs (n = 33 pairs), hereafter referred to as pair type. Disassortative pairs delivered less prey than expected given nestling age, and sexes differed in their respective provisioning effort. In contrast, age-assortative pairs consistently provisioned more, and provisioning effort was comparable between the sexes regardless of parental age. These findings are contrary to studies where older breeders had a greater foraging efficiency and provided young with more prey. Our results indicate that adult age is not an accurate predictor of provisioning in Wood Thrushes and highlight the previously overlooked importance of age-assortative mating on parental investment in this system.
Coexistence of epidermal growth factor receptor 19 deletion and 21 point mutation in nonsmall cell lung cancer: A report of 3 cases

The coexistence of an epidermal growth factor receptor (EGFR) 19 deletion and 21 point mutation represents a rare event in patients with nonsmall cell lung cancer. We present three cases of female patients with lung adenocarcinoma who had the double genetic mutations. The patients were all treated with EGFR tyrosine kinase inhibitors (TKIs) because the tumors were judged inoperable. In all cases, tumor progression occurred after a few months. Further studies are needed to determine whether the EGFR-TKI resistance time in patients with double genetic mutations is longer than that in patients with a single mutation.
Response of organic manure with combination of micronutrient on vegetative growth and yield of strawberry ( Fragaria x ananassa Dutch) cv. Chandler

An experiment was conducted in the department of horticulture, Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad during rabi season (2016-17). The experiment was laid out in RBD having 13treatments and 3replication. The treatment T4 (RDF + Vermicompost 5t/ha + Neem Cake 4t/ha) was found significantly superior compared to other treatment combinations, which recorded highest mean value of plant height (21.20cm), plant spread (26.62cm), number of leaves per plant (16.23), petiole length (13.93cm), number of fruits per plant (4.20) and average fruit weight (19.51g). The highest yield per plant (286.56g) and yield per hectare (17.19t/ha) werealso obtained from treatment T4 (RDF + Vermicompost 5t/ha + Neem Cake 4t/ha) followed by T3 (RDF +Vermicompost 5t/ha + Neem Cake 2t/ha) and lowest yield was obtained from T0 (control).
The Roles of Trophic Interactions, Competition and Landscape in Determining Metacommunity Structure of a Seed-Feeding Weevil and Its Parasitoids

Community composition is determined by attributes of the environment, individual species, and interactions among species. We studied the distributions of a seed weevil and its parasitoid and hyperparasitoid wasps in a fragmented landscape. The occurrence of the weevil was independent of the measured attributes of the landscape (patch connectivity and resource availability). However, between habitat-patch networks, weevil density decreased with increasing parasitism, suggesting top-down control, especially in the north. Parasitism was mostly due to a specialist and a generalist that appeared to compete strongly. This competitive interaction was strongest at high patch-connectivity, perhaps due to a trade-off of local competitive ability and dispersal. Finally, the abundance of the generalist hyperparasitoid was unrelated to landscape or host-species abundance. The snapshot presented by these data can best be explained by top-down effects, interactions among species, host ranges, and patch configuration in the landscape, but not by local host-plant abundance.
Caractérisation moléculaire et fonctionnelle des gènes impliqués dans la mise en place et la lecture de la méthylation d'histones chez l'Arabidopsis thaliana

La methylation des histones constitue un niveau important de controle epigenetique chez les eucaryotes. Mes etudes portent sur la caracterisation des facteurs potentiellement intervenant dans la mise en place et la lecture de la methylation pour mieux apprecier son role et des mecanismes sous-jacents dans la regulation de la transcription et du developpement des plantes chez l’Arabidopsis thaliana. Ainsi, la premiere partie de mes travaux de these a contribue a l’etude d’une proteine a domaine SET (SET DOMAIN GROUP7, SDG7) et a montrer que SDG7 est necessaire au bon deroulement de l'induction de VIN3 et du processus de vernalisation pour la floraison. Nos resultats suggerent que SDG7 pourrait methyler une proteine non-histone encore inconnue dans la regulation de la transcription et le controle de la duree de vernalisation. La deuxieme partie de ma these porte sur l’etude de SDG8 et les H2B-UBIQUITIN-ligases HUB1/HUB2 pour examiner un cross-talk eventuel entre la trimethylation de H3K36 (H3K36me3) et la monoubiquitination d’H2B (H2Bub1). Nous avons montre que H3K36me3 et H2Bub1 sont deposes largement independamment, qui differe d’une dependance hierarchique de deposition prealablement observee chez la levure. La derniere partie de ma these a permis l’identification des proteines HUA2/HULK2 a domaine PWWP comme lecteurs eventuels de H3K36me3 dans la regulation de la floraison et du developpement des plantes.
Brassinosteroids roles and applications: an up-date

Abstract Brassinosteroids are plant steroidal compounds involved in many functions related with plant development, metabolism, signalling and defense against a wide range of biotic and abiotic stresses. Plant architecture, which has a major effect on crop yield, is strongly influenced by brassinosteroids action. Brassinosteroids are recognized as key regulators of plant growth and development involved in a broad spectrum of processes at the molecular, cellular, and physiological levels. These roles suggest that many of the constraints of present agricultural production might be alleviated by manipulation of genetic determinants dealing with brassinosteroids, as well as by its exogenous application. Brassinosteroids are natural, nontoxic, non-genotoxic, biosafe, and eco-friendly, and can therefore be used in agriculture and horticulture to improve the growth, yields, quality, and tolerance of various plants to biotic and abiotic stresses. The present paper comprehensively reviews the latest results in the field of brassinosteroids and envisages future impacts in agriculture.
Assessing among‐lineage variability in phylogenetic imputation of functional trait datasets

Phylogenetic imputation has recently emerged as a potentially powerful tool for predicting missing data in functional traits datasets. As such, understanding the limitations of phylogenetic modelling in predicting trait values is critical if we are to use them in subsequent analyses. Previous studies have focused on the relationship between phylogenetic signal and clade‐level prediction accuracy, yet variability in prediction accuracy among individual tips of phylogenies remains largely unexplored. Here, we used simulations of trait evolution along the branches of phylogenetic trees to show how the accuracy of phylogenetic imputations is influenced by the combined effects of 1) the amount of phylogenetic signal in the traits and 2) the branch length of the tips to be imputed. Specifically, we conducted cross‐validation trials to estimate the variability in prediction accuracy among individual tips on the phylogenies (hereafter ‘tip‐level accuracy’). We found that under a Brownian motion model of evolution (BM, Pagel't λ = 1), tip‐level accuracy rapidly decreased with increasing tip branch‐lengths, and only tips of approximately 10% or less of the total height of the trees showed consistently accurate predictions (i.e. cross‐validation R‐squared >0.75). When phylogenetic signal was weak, the effect of tip branch‐length was reduced, becoming negligible for traits simulated with λ < 0.7, where accuracy was in any case low. Our study shows that variability in prediction accuracy among individual tips of the phylogeny should be considered when evaluating the reliability of phylogenetically imputed trait values. To address this challenge, we describe a Monte Carlo‐based method that allows one to estimate the expected tip‐level accuracy of phylogenetic predictions for continuous traits. Our approach identifies gaps in functional trait datasets for which phylogenetic imputation performs poorly, and will help ecologists to design more efficient trait collection campaigns by focusing resources on lineages whose trait values are more uncertain.
Molecular basis of the nitrogen response in plants

ABSTRACT Nitrogen is an essential element for living organisms because it is a crucial constituent of biomolecules. Inadequate supply of usable nitrogen reduces plant growth and crop yield. The primary nitrogen sources for plants are nitrate and ammonium in soils, and plants have multiple layers of sensing and adaptive mechanisms that respond to the availability of these nutrients. The adaptive responses are called ‘nitrogen responses,’ which include morphological and physiological responses enabling plants to efficiently take up nitrogen and adapt to spatiotemporal fluctuations in nitrogen abundance in the field. In this review, we summarize the strategies that plants use to respond to changes in the nitrogen nutrient status in the soil and discuss different effects produced by nitrate and ammonium, emphasizing the important role of nitrate for plant growth. Recent studies revealed the molecular mechanism mediating the primary response to nitrate provision and the molecular mechanisms that coordinate the nitrogen response with responses to another macronutrient, phosphorus. We thus discuss these molecular mechanisms as well.
Effects of Repeated Restraint Stress on Tissue Metabolism in Rats.

It has been reported that repeated restraint stress (RS), 3 hours/day for 3 days, in rats caused sustained weight loss and a temporary drop in daily food intake with no subsequent compensatory overeating during the post stress period. The hypothesis tested in the present study is that RS causes peripheral tissue metabolism changes which account for the abnormal regulation o f body weight and food intake during the post stress period. Adult male Sprague Dawley rats were assigned to control, pair fed (PF) or RS groups. One day after the end o f RS, midbrain urocortin mRNA was at control levels in RS rats, but elevated in PF rats. NPY content in hypothalamus PVN was the same for all groups. These results confirm that the acute effects of stress were already reversed one day after stress. The initial weight loss during stress was lean tissue, but 5 days post­ stress, it was both lean and fat. In an oral glucose tolerance test one day after RS, insulin release was blunted but glucose clearance was normal. A number of measurements for lipid and glucose metabolism were made in peripheral tissues. The major differences in RS rats were a substantial inhibition of adipocyte, but not muscle, glucose transport. In contrast, adipocyte fatty acid oxidation was increased. In the liver, there was an increment of hepatocyte glucose transport in RS rats. This extra glucose was stored as a glycogen in the liver. P-adrenergic receptor number was increased in adipose but not in liver from RS rats, which implies that lipolysis was increased in RS rats. These results demonstrate that RS affected nutrient partitioning and specific tissue nutrient metabolism during the post stress period. The increased glucose uptake and storage in liver may contribute to the absence of compensatory hyperphagia in