Miracle-dz/UniFAR-FTUs huggingface dataset:
Article (refereed) - postprint Can on-site management mitigate nitrogen deposition impacts in non-wooded habitats?

Nitrogen (N) deposition is a major cause of plant biodiversity loss, with serious implications for appropriate management of protected sites. Reducing N emissions is the only long-term solution. However, on-site management has the potential to mitigate some of the adverse effects of N deposition. In this paper we review how management activities such as grazing, cutting, burning, hydrological management and soil disturbance measures can mitigate the negative impacts of N across a range of temperate habitats (acid, calcareous and neutral grasslands, sand dunes and other coastal habitats, heathlands, bogs and fens). The review focuses mainly on European habitats, which have a long history of N deposition, and it excludes forested systems. For each management type we distinguish between actions that improve habitat suitability for plant species of conservation importance, and actions that immobilize N or remove it from the system. For grasslands and heathlands we collate data on the quantity of N removal by each management type. Our findings show that while most activities improve habitat suitability, the majority do little to slow or to reduce the amount of N accumulating in soil pools at current deposition rates. Only heavy cutting/mowing with removal in grasslands, high intensity burns in heathlands and sod cutting remove more N than comes in from deposition under typical management cycles. We conclude by discussing some of the unintended consequences of managing specifically for N impacts, which can include damage to non-target species, alteration of soil processes, loss of the seedbank and loss of soil carbon.
Improvement of resistance to bacterial blight through marker assistedbackcross breeding and field validation in rice (Oryza sativa)

Bacterial blight is one of the major constraints in rice cultivation. Breeding for durable resistance is most effective and economical method to combat disease. In present study, four resistance genes (Xa4, xa5, xa13 and Xa21) were pyramided into popular cv. Mahsuri and two hybrid rice parental lines, PRR78 and KMR3 using marker assisted back cross breeding. Nine pyramid families of each background were evaluated under both artificial and natural disease conditions. Pyramids were inoculated with sixteen Xanthomonas oryzae pv. oryzae isolates collected from different parts of India. BF16 was highly virulent on recurrent parents with a yield loss of 23% in Mahsuri, 28% in PRR78 and 24% in KMR3. BF7 (10% loss in Mahsuri and 13% in KMR3) and BF10 (22% in PRR78) were least virulent. Under natural condition at Maruteru, disease showed a yield loss of 22% in Mahsuri, 28% in PRR78 and 26% in KMR3. Under both conditions, none of the pyramids were susceptible. There were no significant differences within pyramids with respect to any character evaluated. No pyramid was susceptible. The agronomic characters showed no significant difference between parent and pyramid. Yield and its related characters were statistically significant between parents and pyramids (P< 0.05). The pyramids insulated a heavy yield loss to the tune of ~28% and pyramiding of resistance genes (two dominant and two recessive) did not show any negative effect on agronomic performance of any pyramid. These pyramids can be used directly and also as valuable source of resistance in future breeding programs.
Biology of the normal breast : Relation to mammographic density and risk of breast cancer

Increased understanding of the variability in normal breast biology will enable us to identify mechanisms of breast cancer initiation and the origin of different subtypes, and to better predict breast cancer risk. In this pilot study we have explored the variation in gene expression patterns in breast biopsies from 79 healthy women referred to breast diagnostic centers in Norway. Unsupervised hierarchical clustering identified 12 samples consistently clustering tightly together (cluster 1) regardless of clustering algorithm and gene filtering used. Genes upregulated in cluster 1 samples code for proteins involved in extracellular matrix, vascular development, response to hormones and metabolism. Proteins involved in cell-cell junction and plasma membrane were over-represented in the genes down-regulated in cluster 1. Validation in a separate dataset consisting of histologically normal tissue from both breasts harboring breast cancer and from mammoplasty reductions identified a similar cluster with up-regulation of the same functional categories. Comparison of the expression profile of the cluster 1 samples with several published gene lists describing breast cells showed that these samples share characteristics with stromal cells and stem cells, and to a certain degree with mesenchymal cells and myoepithelial cells. The samples in cluster 1 share many features with the newly identified claudin-low breast cancer intrinsic subtype, which also shows characteristics of stromal and stem cells. Further studies are needed to fully elucidate the variation in the biology of normal breasts, its relation to breast cancer risk and possible link to the origin of the different molecular subtypes of breast cancer.
Draft Genome Sequence of Terasakiispira papahanaumokuakeensis PH27AT, a Spiral Bacterium from the Northwestern Hawaiian Islands

ABSTRACT The genus Terasakiispira hosts only Terasakiispira papahanaumokuakeensis PH27AT, cultivated from an anchialine pond on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The strain's genome sequence may provide insights into the evolution of free-living Oceanospirillaceae.
Reactive Oxygen Species Regulate Activity-Dependent Neuronal Structural Plasticity in Drosophila

Neurons are inherently plastic, adjusting their structure, connectivity and excitability in response to changes in activity. How neurons sense changes in their activity level and then transduce these to structural changes remains to be fully elucidated. Working with the Drosophila larval locomotor network, we show that neurons use reactive oxygen species (ROS), metabolic byproducts, to monitor their activity. ROS signals are both necessary and sufficient for activity-dependent structural adjustments of both pre- and postsynaptic terminals and for network output, as measured by larval crawling behavior. We find the highly conserved Parkinson’s disease-linked protein DJ-1ß acts as a redox sensor in neurons where it regulates pre- and postsynaptic structural plasticity, in part via modulation of the PTEN-PI3Kinase pathway. Neuronal ROS thus play an important physiological role as second messengers required for neuronal and network tuning, whose dysregulation in the ageing brain and under neurodegenerative conditions may contribute to synaptic dysfunction.
Bioprospecting for culturable actinobacteria with antimicrobial properties isolated from rivers in Colombian Orinoquia

Purpose : To Isolate and characterize Actinobacteria with antimicrobial activity from Guaviare River (Colombia). Methods : Water and sediment samples were collected from Guaviare River. Direct plating, heat and CaCO3 methods were used to isolate Actinobacteria. Six bacterial strains were tested using T-Streak method : Escherichia coli ATCC 23724, Staphylococus aureus ATCC 25923, Acinetobacter baumannii ATCC 19606, Bacillus subtilis ATCC 21556, Klebsiella pneumoniae ATCC 700603, Chromobacterium violaceum ATCC 31532. Strains of Fusarium sp. H24, Trichoderma harzianum H5 and Colletotrichum gloeosporioides were tested using Kirby-Bauer method. Isolates with high antimicrobial activity were selected for further taxonomic identification. Results : A total of 374 actinobacteria isolates were obtained. Seven isolates exhibited high antimicrobial activity (p < 0.05) and were confirmed as members of Streptomycetaceae family. Of these, three isolates showed differential phenotypic and genotypic profiles, indicating that they may represent new species. Conclusions : To date, this is the first study of this type in Colombian Orinoquia and indicates that this promising source of Actinobacteria from aquatic sediments with the ability to produce antimicrobial secondary metabolites. Keywords : Actinobacteria, Antimicrobial activity, Secondary metabolites, Streptomycetaceae, Phenotypic and genotypic profiles, Colombian Orinoquia
Phylogenetic analysis of Western Atlantic Bathygobius (Teleostei: Gobiidae)

The phylogenetic relationships of the Western Atlantic species of Bathygobius are inferred from DNA sequence data from two mitochondrial genes (cytochrome b, cytochrome c oxidase-I) and one nuclear gene (Recombination Activating Gene I). The phylogeny inferred from the concatenated dataset of the three genes uncovered the following major findings: (i) the Western Atlantic species of Bathygobius as a whole are not monophyletic; (ii) a well-supported monophyletic group containing B. soporator, B. lacertus and the Eastern Pacific B. andrei was recovered (termed the B. soporator group); (iii) a well-supported monophyletic group was recovered that contains B. curacao, the Eastern Pacific B. ramosus and B. lineatus, and B. antilliensis (termed the B. antilliensis group); (iv) the relationships between the several lineages of new world Bathygobius and some species of old world Bathygobius could not be resolved, and monophyly of a clade of all new world species could not be determined. The evolutionary history of the Western Atlantic species involves periods of diversification that occurred both before and after the closure of the Isthmus of Panama.
Modulation du trafficking et de la signalisation du récepteur GLP-1 dans la cellule β pancréatique par un traitement chronique aux glucocorticoïdes

Les cellules beta pancreatiques synthetisent et secretent l’insuline, unique hormone hypoglycemiante de l’organisme. Ces cellules jouent un role central dans l’apparition du diabete, preserver leurs masses fonctionnelles est donc essentiel. Le recepteur GLP-1, appartenant a la classe B de la super famille des recepteurs couples aux proteines G (RCPGs), est considere comme une cible therapeutique majeure dans le traitement du diabete de type 2. Via son recepteur, le GLP-1 potentialise la secretion d’insuline en reponse au glucose et favorise la survie des cellules beta. Les glucocorticoides sont des hormones du stress impliquees dans la regulation energetique, largement utilises en therapeutique pour leur proprietes anti-inflammatoire, immunosuppresseur et antiallergique. Neanmoins, les glucocorticoides administres en chronique sont diabetogenes en exercant notamment des effets deleteres sur les cellules beta. Nous avons caracterise l’impact d’une exposition prolongee des cellules beta a un glucocorticoide de synthese (la dexamethasone) sur les actions biologiques du glucose et du GLP-1.Nous montrons qu’une exposition prolongee des cellules beta a la dexamethasone exerce des effets deleteres en inhibant la secretion d’insuline en reponse au glucose et l’activation des kinases de survie ERK1/2 (Extracellular Regulated Kinases 1/2). A l’inverse, nous demontrons que l’exposition prolongee des cellules beta a la dexamethasone favorise le maintien du recepteur GLP-1 a la membrane plasmique, augmente le couplage du recepteur a la proteine Galpha s, ce qui se traduit par une production de second messager (AMPc) intracellulaire doublee. Malgre une diminution des effets du glucose, la secretion d’insuline et l’activation des kinases ERK1/2 en reponse au GLP-1 ne sont pas affectees. Cette etude revele qu’une exposition chronique des cellules beta aux glucocorticoides 1) regule le trafficking du recepteur GLP-1 et favorise son maintien a la surface cellulaire, 2) hypersensibilise la signalisation du recepteur GLP-1 dependante de la proteine Gαs , et 3) pourrait impacter les effets therapeutiques des molecules ciblant l’activation du recepteur GLP-1.
Typification of three European species epithets attributable to Strobilomyces (Boletales)

One of the most easily recognized genera of boletes is Strobilomyces, represented by taxa on most continents. At least in the Northern Hemisphere, early European species epithets are being applied to local taxa. Among these epithets in common use are S. strobilaceus and S. floccopus, sanctioned (as Boletus) by Fries. Contemporary with these is also Boletus strobiliformis, although not sanctioned. All three names, however, have been without acceptable type specimens, so identifications and diagnoses have remained insecure. This paper designates type specimens for these epithets as a prerequisite for accurate assessment of taxa. Comparison of morphological characters and sequences of ITS region of nrDNA gathered from type and additional material suggest existence of only a single European species, correctly named S. strobilaceus.
Molecular Cloning and Expression of Recombinant Phage Antibody against Fumonisin B1.

Bacteriophage expression systems offer promise for the development of novel antibody reagents applicable to detection of microbial agents and their toxins in foods. In this study, fumonisin B1 (FB1)-specific antibodies, composed of a single chain containing a variable heavy (VH) and light (VL) chain fragments (ScFv), were cloned using mRNA from either spleen cells of mice immunized with FB1-BSA conjugate or from an existing hybridoma cell line that produces anti-FB1 antibody. The approach consisted of (i) reverse transcription of isolated mRNA, (ii) polymerase chain reaction amplification of VH and VL cDNAs, (iii) ligation of VL and VH chains, and (iv) expression of ScFv proteins on the surface of a filamentous bacteriophage or as a soluble fragment. The efficacy of using the recombinant ScFv proteins for the detection of FB1 were evaluated in a competitive indirect enzyme-linked immunosorbent assay (CI-ELISA). Compared to polyclonal or monoclonal antibodies for FB1, the recombinant ScFv proteins were 10 to 100 times less sensitive in the CI-ELISA. The secreted ScFv protein did not cross-react with FB2 or FB3. The results indicated that production of a recombinant antibody to a mycotoxin is feasible. However, problems associated with the affinity or avidity of ScFv fragments need to be further addressed before this technology is adaptable to the development of improved immunodiagnostic kits for mycotoxins or other food borne disease hazards.
In Vitro Antioxidant Activity of Randia Dumetorum Lam Leaf Extract

Antioxidant activity of ethanolic extract of Randia dumetorum leaves were carried out for proving its utility in free radical mediated diseases including diabetic, cardiovascular, cancer etc. The ethanolic extract was screened for in vitro antioxidant activity by oxygen radical scavenging such as DPPH, total antioxidant assay, superoxide metal chelation and iron reducing power activity at different concentrations. Throughout the studies leaves extract showed marked antioxidant activity. The antioxidant activity of the leaves extract may be due to the phytochemicals present in it. The antioxidant activity was found to be concentration dependent and may be attributed to the presence of bioflavonoids content in the leaves of Randia dumetorum. Overall, the plant extract is a source of natural antioxidants which might be helpful in preventing the progress of various oxidative stress mediated diseases including aging.
A new and unusual shrew (Soricidae) from the Miocene of Colorado and South Dakota

The Hemingfordian deposits of southwestern South Dakota and northeastern Colorado have yielded an unusual heterosoricine shrew, Wilsonosorex n. gen. Two new species, Wilsonosorex conulatus and Wilsonosorex bateslandensis, possess both a paraconule and metaconule on the upper molars. This tooth structure is usually considered to be a primitive trait and suggestive of a relict form. However, the obvious affinities of this shrew to the genus Heterosorex appear to indicate a newly acquired character.
Methods of controlled ovarian stimulation for embryo/oocyte cryopreservation in breast cancer patients

ABSTRACT Introduction: Controlled ovarian stimulation (COS) is a crucial step before oocyte collection and subsequent embryo/oocyte cryopreservation. However, in young breast cancer patients, the need for COS raises specific issues that should be taken into account during oncofertility counseling. Areas covered: We aim to perform an overview of COS protocols with a specific focus on the current knowledge and clinical challenges related to their use in young breast cancer patients. Expert commentary: Many protocols for COS are currently available to induce multiple follicular recruitment and maximize oocyte retrieval in women undergoing in vitro fertilization treatment. In cancer patients, to avoid the need to wait for a spontaneous menstruation, emergency protocols are also available so that COS can be started at any time during the menstrual cycle. COS protocols with the addition of tamoxifen or letrozole have been specifically designed for breast cancer patients to limit the potential negative impact of the temporary increase in estradiol levels during stimulation.
Phylogeography of the pelagic fish Seriola lalandi at different scales: confirmation of inter-ocean population structure and evaluation of southern African genetic diversity

The study investigated the global and regional phylogeography of the yellowtail kingfish Seriola lalandi by examining genetic diversity and population genetic structure of this species at inter-and intra-ocean level and on a regional scale. DNA fragments of two mitochondrial genes, cytochrome b (Cytb) and cytochrome c oxidase subunit I (COI) and one nuclear gene, recombination activating gene 1 (RAG1), were sequenced to investigate the global-scale phylogeography of this species. The population genetic structure within the South Pacific, as well as along the South African coastline, was examined further using six microsatellite markers. Three distinct clades were identified for S. lalandi, which correspond with previously described subspecies of the North-East Pacific, North-West Pacific and the Southern Hemisphere. Within the latter, additional divergence was observed between the South Pacific and the South-East Atlantic regions. Divergence estimates were indicative of a Pacific origin for S. lalandi populations, because of Pleistocene vicariant events. Microsatellite analyses revealed overall significant genetic differentiation between South African and South Pacific samples. This corroborates recent findings on the global phylogeography of the species. No population differentiation was observed within South Africa, indicating high levels of gene flow.
Embryo rescue of early ripening plum cultivars

Embryoculture are an efficient in vitro method finding application in breeding of early ripening stone fruit species. The aim of the present study was to obtain seedlings of early ripening plum cultivars, included in the breeding programmes of the Fruitgrowing Institute – Plovdiv, by optimizing the nutrient media. Seeds isolated from ripen fruits of cvs ‘Burmosa’ (Prunus salicina L.) and ‘Ruth Gerstetter’ (Pr. domestica L.) were used. After sterilizing the seeds, the embryos were isolated and cultivated on variants of MS nutrient medium (Murashige & Scoog, 1962). The effect of the hormonal and carbohydrate content of the medium was tested. ‘Burmosa’s embryos demonstrated 70-100% germination capacity on all the nutrient media. For the embryos of cv. ‘Ruth Gerstetter' the best germination of 75% was achieved on 2.5 μM IBA and 7.5 μM TDZ, containing as a carbohydrate source 2% of sorbitol and 2% of sucrose. On media containing TDZ, along with the development of the zygote embryo, adventitious organogenesis was also observed. As a result of the study over 300 seedlings were obtained which were adapted and planted in a breeding nursery. INTRODUCTION The main problem in plum (Prunus domestica L.) breeding is the development of early ripening, disease resistant cultivars, producing high quality fruits. The solution of this problem would enable the extension of harvest period and the produce realization at higher market prices. At the same time, the breeding of early cultivars creates problems for the dying of their embryos. As female parents, only medium early and late cultivars can be used, which decreases the share of the progeny possessing the target traits. A key for solving these problems is the combination of conventional with biotechnological methods and with embryo cultures, in particular. In vitro cultivation of isolated embryos is an effective approach used in breeding for earliness in stone fruit species cherries, peaches, plums, apricots, etc. The effectiveness of the method is influenced by a number of factors, such as embryo size at the moment of isolation, medium composition, duration of low temperature treatment, culture conditions, etc.(Ramming, 1990). The objective of the present study was to develop seedlings of early plum cultivars, involved in the breeding programmes of the Fruit Growing Institute in Plovdiv. MATERIAL AND METHODS
Porins of Pseudomonas £uorescens MFO as ¢bronectin-binding proteins

Bacterial adherence is a complex phenomenon involving specific interactions between receptors, including matricial fibronectin, and bacterial ligands. We show here that fibronectin and outer membrane proteins of Pseudomonas fluorescens were able to inhibit adherence of P. fluorescens to fibronectin-coated wells. We identified at least six fibronectin-binding proteins with molecular masses of 70, 55, 44, 37, 32 and 28 kDa. The presence of native (32 kDa) and heat-modified forms (37 kDa) of OprF was revealed by immuno-analysis and the 44-kDa band was composed of three proteins, their N-terminal sequences showing homologies with Pseudomonas aeruginosa porins (OprD, OprE1 and OprE3). > 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Use of NMR spectroscopy in the analysis of carnosine and free amino acids in fermented sausages during ripening

Quantitative changes of carnosine and free amino acids in high-fat (43–50 mass %) fermented sausages during ripening were analysed using a 600 MHz VNMRS NMR spectrometer. Seven free amino acids were identified in the samples and a relatively high content of carnosine was observed in the final stage of ripening. The NMR method for the determination of free amino acids and carnosine content applied in this work has been used for the first time and it has proven to be suitable for the analysis of fermented sausages.
Floristic studies on algae from inland waters of Ongul Islands and vicinity, Antarctica. I: East Ongul Island

A freshwater algal flora of East Ongul Island is described. Total 31 taxa were found in algal mat samples: Cyanophyceae, 20 species; Bacillariophyceae, 4 species and Chlorophyceae, 7 taxa. Altogether a total 34 taxa were recorded from water and mat samples examined in the present study. Cyanophyceae was most abundant in the number of species representing some 65%