Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic and taxonomic delimitation of the cyanobacterial genus Aphanothece and description of Anathece gen. nov.

The traditional cyanobacterial form-genus Aphanothece was established according to morphological criteria in the middle of the 19th century by Nägeli. It comprises unicellular morphotypes with oval or cylindrical cells arranged irregularly in amorphous mucilaginous colonies. Up to now, more than 80 morphospecies have been described, mostly from various freshwater aquatic habitats. The genus Aphanothece is heterogeneous in the traditional morphological concept as well as according to modern molecular criteria. Therefore, it must be divided into several taxonomic clusters. Generic characteristics, studied by a combination of molecular sequencing of 16S rDNA, ultrastructure, ecology and morphological variation, were investigated in selected strains and populations of type species of the traditional subgenera Aphanothece and Anathece. Distinct differences were found between both of these clusters in their position in the phylogenetic tree, ultrastructure of cells, morphology (size of cells), mucilage structure, life cycles and ecology. They must therefore be separated into two genera, according to both bacteriological and botanical criteria, and placed in different orders (Chroococcales and Synechococcales). Accordingly we describe Anathece, gen. et stat. nov., and transfer to it the type A. clathrata comb. nov. and six other species. Several other morphotypes, originally classified in the genus Aphanothece (but morphologically different from Aphanothece sensu stricto), correspond to the genera Cyanoaggregatum, Cyanogastrum, Gloeobacter, Gloeothece and Halothece. The closest relative of Anathece appears to be Cyanobium.
Injectable Colloidal Gold for Use in Intrafractional 2D Image‐Guided Radiation Therapy

In the western world, approximately 50% of all cancer patients receive radiotherapy alone or in combination with surgery or chemotherapy. Image‐guided radiotherapy (IGRT) has in recent years been introduced to enhance precision of the delivery of radiation dose to tumor tissue. Fiducial markers are often inserted inside the tumor to improve IGRT precision and to enable monitoring of the tumor position during radiation therapy. In the present article, a liquid fiducial tissue marker is presented, which can be injected into tumor tissue using thin and flexible needles. The liquid fiducial has high radio‐opacity, which allows for marker‐based image guidance in 2D and 3D X‐ray imaging during radiation therapy. This is achieved by surface‐engineering gold nanoparticles to be highly compatible with a carbohydrate‐based gelation matrix. The new fiducial marker is investigated in mice where they are highly biocompatible and stable after implantation. To investigate the clinical potential, a study is conducted in a canine cancer patient with spontaneous developed solid tumor in which the marker is successfully injected and used to align and image‐guide radiation treatment of the canine patient. It is concluded that the new fiducial marker has highly interesting properties that warrant investigations in cancer patients.
Dose responses of tsetse flies (Glossina) to carbon dioxide, acetone and octenol in the field

ABSTRACT Studies were conducted in Zimbabwe of the catch of Glossina pallidipes Austen from an electric net plus target baited with mixtures of acetone plus carbon dioxide or 1‐octen‐3‐ol (octenol) plus carbon dioxide. For acetone dispensed alone at 5–50, 000 mg h‐1, ten‐fold increments in the dose increased the catch 1.7 times. For carbon dioxide dispensed alone, dose increments from 12 to 1201 h‐1 doubled the catch, but the catch was not further increased by dispensing carbon dioxide at 600–1200 1 h‐1. For mixtures of these two odours, ten‐fold increments in the dose of carbon dioxide between 12 and 12, 0001 h‐1 increased the catch c. 2.5 times if acetone was also dispensed at >50 mg h‐1; changes in the dose of acetone between 50 and 50 000 mg h‐1 did not affect the catch. The addition of octenol (0.05 mg h‐1) to carbon dioxide (12–12001 h‐1) doubled the catch. Ten‐fold increments in the dose of octenol between 0.05 and 5 mg h‐1 did not increase the catch significantly and the catch was independent of changes in the dose of carbon dioxide between 120 and 12001 h‐1. The behavioural basis of the dose‐response curves was investigated using an incomplete ring of electric nets to assess the flight orientation of tsetse in different odours. Upwind flight was not elicited by acetone or octenol alone, or by carbon dioxide unless it was at very high doses, however, mixtures of carbon dioxide with acetone or octenol elicited upwind flight. It is suggested that the attractiveness of mixtures of acetone and carbon dioxide is a function of the region of overlap of these two odours at above threshold concentration. Acetone and octenol on their own appear to increase the responsiveness of flies to visual cues.
Production of Extracellular L-Asparaginases by Microorganisms

A variety of microorganisms were tested for their extracellular l-asparaginase productivity and it was found that many bacteria, fungi and yeasts are positive for it. Especially some strains in the genera Pseudomonas, Candida and Rhodotorula were able to produce a large amounts of the enzyme. Escherichia coli, however, that contained intracellular enzyme was unable to produce extracellular one. In enzymological properties some differences were noted among these extracellular enzymes. Pseudomonas asparaginase showed glutaminase activity too, but the asparaginases of Candida and Rhodotorula were unable to hydrolyze glutamine. Candida l-asparaginase was most stable to heat-treatment.
Previous infestation of pea aphids Acyrthosiphon pisum on broad bean plants resulted in the increased performance of conspecific nymphs on the plants

Abstract We studied the effects of previous infestation of broad bean plants by pea aphids Acyrthosiphon pisum on the performance of conspecific nymphs on the plants and the involvement of jasmonic acid (JA)-related defenses. The time needed for newly emerged nymphs to become reproductive adults on broad bean plants previously infested by conspecifics (pre-infested plants) was significantly shorter than on uninfested (control) broad bean plants. The total numbers of nymphs produced by aphids on preinfested and control plants were not significantly different. Preinfested plants produced significantly less endogenous JA than that control plants did. To test the effect of JA decreases, we conducted experiments on the developmental duration of nymphs on broad bean plants treated with JA (JA-treated plants) before infestation. The time needed for nymphs to become reproductive adults on JA treated preinfested broad bean plants was not significantly different from that on JA-treated control plants. The results suggested a possible parental care by pea aphids: the adult aphids manipulated JA-related defenses in broad bean plants that had positive effects for their offspring.
A species of Cryptonemia new to Europe

The morphology, reproduction and seasonal variation of a large foliose species of Cryptonemia collected in the drift in 1971–73 at Cork Harbour, Republic of Ireland, is described and compared with the known species of the genus. Although obviously closely related to a group of foliose Pacific species: C. borealis Kylin, C. obovata J. Ag. and C. angustata (Setch. et Gardn.) Dawson, the Irish Cryptonemia is not completely identifiable with any one of these and is therefore described as C. hibernica sp. nov., pending a revision of the genus.
Molecular Modelling and Functional Studies of the Non-Stereospecific α-Haloalkanoic Acid Dehalogenase (DehE) from Rhizobium SP. RC1 and its Association with 3-Chloropropionic Acid (β-Chlorinated Aliphatic Acid)

ABSTRACT Many environmental pollutions are caused by the abundance of xenobiotic compounds in nature. For instance, halogenated compounds released from chemical industries were proven to be toxic and recalcitrant in the environment. However, haloalkanoic acid dehalogenases can catalyse the removal of halides from organic haloacids and thus have gained interest for bioremediation and synthesis of industrial chemicals. This study presents the first structural model and the key residues of the non-stereospecific haloalkanoic acid dehalogenase, DehE, from Rhizobium sp. RC1. The enzyme was built using a homology modelling technique; the structure of DehI from Pseudomonas putida PP3 was used as a template, because of its homology to DehE. The structure of DehE consists of only α-helices. Twelve conserved residues that line the active site were identified: Trp34, Ala36, Phe37, Asn114, Tyr117 Ala187, Ser188, Asp189, Tyr265, Phe268, Ile269, and Ile272. These residues are consistent with the residues found in the active site of DehI and D, L-DEX 113 from Pseudomonas sp. 113. Asp189 activates the water molecule as a nucleophile to attack the substrate chiral centre, which would result in an inversion of configuration of either D- or L-substrates. Both D- and L-substrates bind to and interact with the enzyme by hydrogen bonding with three residues, Trp34, Phe37, and Ser188. In addition, a putative tunnel was also identified that would provide a channel for the substrate to access the binding site. Based on computational analysis, DehE was proven to have the substrate affinity towards 3-chloropropionic acid (3CP)/β-chlorinated aliphatic acid, however, its dehalogenation process is far from clear. This DehE structural information will allow for rational design of non-stereospecific haloalkanoic acid dehalogenases in the future.
Legumes—Past, Present, and Future

The term legume (from the Latin legere, to gather), although botanically meaning the seed pod itself, is applied both to the fruit or seed and to the plant or plant family-in the latter case, somewhat nonspecifically. More commonly, it refers to the subfamily Papilionoideae, the largest by far of the three subfamilies; it frequently refers more specifically to those herbaceous plants within the subfamily that are of agronomic significance. The other two subfamilies, Caesalpinioideae and Mimosoideae, are represented largely by tropical or subtropical trees or herbaceous plants. Although of interest and of potential economic importance, they will not be dealt with extensively here. The Leguminosae probably originated in the late Jurassic period and saw great expansion and diversification in the Cretaceous, stimulated by, participating in, or perhaps contributing to the striking and as yet ill-described geochemical and geobiological changes that characterized that period.
Characterization of ubiquitinated lysosomal membrane proteins in acanthamoeba castellanii

Ubiquitinated proteins in lysosomes were characterized by using two monoclonal antibodies (mAbs): LYS8–1, a mAb to lysosomal proteins, and NYA124, a mAb to ubiquitin. LYS8–1 stained lysosome‐like vesicles in immunofluore‐scence microscopy of Amoeba proteus and Acanthamoeba castellanii. In immunoblotting, LYS8–1 ‘s antigens (LYS proteins) were detected as 68‐kDa and 77‐kDa proteins in A. proteus, and as 30‐kDa and 39‐kDa proteins in A. castellanii. In immunoprecipitation of A. castellanii, at least four distinct LYS proteins, LYS35p, LYS39p, LYS42p, and LYS46p, were detected and accumulated upon inhibition of lysosome functions but not upon that of 26S proteasome functions. They were all found to be ubiquitinated, and were recovered in the lysosome fractions in subcellular fractionation experiments. In chemical fractionation analyses, LYS35p and LYS39p were demonstrated to be peripherally associated with lysosome membrane, while LYS42p and LYS46p tightly bound to the membrane. These results suggest that the LYS proteins become associated to lysosomal membrane upon ubiquitination.
Effects of arsenic on reactive oxygen species and antioxidant defense system in tomato plants

In this study, the generation of reactive oxygen species, the induction of oxidative stress, and the response of the antioxidative system in hydroponically grown tomato plants as the cause of arsenic-induced phytotoxicity are investigated. Reduction in plant growth was measured in terms of dry weight and length of roots and shoots, the latter accumulating more arsenic than the roots. The treatment resulted in increased formation of superoxide anion (O2.−), H2O2, and thiobarbituric acid reactive substances, which indicate augmented lipid peroxidation. Superoxide dismutase, catalase (CAT), and ascorbate peroxidase activities were increased in arsenic-treated tomato plants while CAT activity was insignificantly increased.
Differentially Expressed Forms of 1-L-myo-Inositol-1-Phosphate Synthase (EC) in Phaseolus vulgaris*

We have characterized two distinct polypeptides with 1-L-myo-inositol-1-phosphate synthase (MI-1-P synthase) activity that are differentially expressed during development in Phaseolus vulgaris. Western analyses, enzyme assays, and partial purification of MI-1-P synthase during embryonic and postembryonic development show that its expression is temporally and spatially regulated. Developmental Western analyses of soluble proteins detect a small protein, approximately 33 kDa, with MI-1-P synthase activity during the globular stage (stage II) of embryogenesis and in mature roots. Expression of this small protein is also enriched in thylakoidal membranes of fractionated leaf chloroplasts, although Western analyses of total soluble leaf proteins show no cross-reacting material. In contrast, a larger protein, approximately 56 kDa, with MI-1-P synthase activity is present during the cotyledonary phase (stage IV) of embryogenesis in green cotyledons of seedlings and in young roots.
Determining the Hydraulic Geometry Parameters of Seyhan River

Cross-section of rivers vary by time due to the dynamic structure of hydraulic geometry. The hydraulic geometry parameters of rivers including the width, depth and velocity are related to its discharge as simple power functions at a given cross-section. The characteristics of a river can be determined by using the hydraulic geometry parameters. The aim of this study is to determine the downstream and at-a-station hydraulic geometry parameters of Seyhan River. The hydraulic geometry parameters are estimated by employing the daily discharge values and the cross-sectional data of seven flow measurement stations located on the main river and its tributaries. The results of the analyses show that both the summation of the exponents and the multiplication of the coefficients are almost unity. These outcomes are expected to be helpful in developing water resources projects the basin.
Do soil nutrients mediate competition between grasses and Acacia saplings

The structure and composition of savanna vegetation is influenced by resource availability and disturbance. Grasses, a major component of savanna systems, influence the tree-grass balance by competing with trees for light, water and soil nutrients as well as providing fuel for fires. Overgrazing, and the ensuing decreased grass competition and fire effects resulting from diminished grass vigor and cover, are thought to be major drivers of bush encroachment. To investigate impacts of competition from grass on saplings of Acacia karroo Hayne. and Acacia nilotica (L.). Willd. ex. Del. under high and low soil fertility, six grass species, Aristida junciformis (Trin & Rupr.), Eragrostis capensis (Thunb.) Trin. , Hyparrhenia hirta Stapf. , Panicum maximum Jacq. , Sporobolus africanus (Poir.) Robyns & Tournay and Themeda triandra Forssk. , were planted in pots with a tree sapling as the central test species. The major competitive effects experienced by tree saplings were dependent on nutrient level and the identity of the competing grass species (P < 0.001). Aboveground A. karroo was more strongly affected by grass competition under high nutrient conditions, whereas an increase in nutrient level had little effect on the competition between A. nilotica and the grasses (P < 0.001). Acacia karroo was also strongly affected by grass competition belowground; however, the opposite trend was observed for A. nilotica (P < 0.001). Eragrostis capensis was one of the most competitive grass species, reducing sapling aboveground biomass by 85% and 65% under high and low nutrient conditions, respectively, and sapling belowground biomass by 71% on average. Increasing nutrient availability resulted in an increase in competition exerted on A. karroo by all grasses but little to no change for A. nilotica. Changes in savanna composition and structure are thus likely to be influenced by grass species composition and soil nutrient status.
Estudio comparativo del splicing alternativo del gen NCR3 en diferentes especies de mamíferos y sus posibles implicaciones funcionales

Alternative splicing (AS) is a major source of transcriptome and proteome diversity in higher eukaryotes allowing the generation of several structurally and functionally distinct mRNAs and protein isoforms from a single gene. Differential AS variants expression has been implicated in tissue and cellular differentiation, which in an evolutionary context could account for the phenotypic divergence of mammals that share a common repertoire of genes. On the other hand, the miss-regulation of AS is one of the mayor sources of human disease. However, there are not many detailed comparative analyses showing the alternative splice forms generated from particular genes among different organisms. The work presented here is a deep study of the splice variants expressed by the ? Natural Cytotoxicity Receptor 3? (NCR3) gene and its comparative analysis among 13 mammals. NCR3 is a member of the NCR family, which represents the major NK cells triggering receptors. It has been involved in the recognition and killing of tumoral and infected cells, and in the maturation of dendritic cells. By using a combination of nested RT-PCR and RNA-seq analysis, it was possible to detect the expression of several NCR3 transcripts in all the analysed mammalian species, except in Mus musculus, where NCR3 is a pseudogen. It was observed an increase in the number of coding variants in primates, mainly by the internal splicing of exon 2 and the presence of exons 4II and 4III, which are only expressed in higher primates (Hominoidea). In contrast, the diversity of non-coding variants is similar among all analysed species, although there are some conserved ones, which could have a potential regulatory role. The nine human splice variants, six coding and three non-coding, were only detected at high expression levels in immune-related tissues, being the coding A, B y C the most abundant ones. The predicted human protein isoforms are potential transmembrane type I receptors, which extracellular domains are predicted to be Immunoglobulin type V (IgV) or type C (IgC). The interaction of these potential NCR3 extracellular domains with the ligand B7-H6 was analysed using flow citometry assays. Firstly, they were over-expressed in insect cells finding that defective glycosylation avoids binding. In a second approach, it was used a mammalian system detecting only specific binding of IgV domain to B7H6, indicating that B7H6 is not a ligand for IgC containing isoforms. In conclusion, all the presented data suggest a potential role of AS in the NCR3 functions and immune system regulation and evolution. keywords: RNA Splicing Alternative Splicing RNA-seq NGS NCR3 NKp30 NKs cells B7H6
Improved retrieval of land ice topography from CryoSat-2 data and its impact for volume-change estimation of the Greenland Ice Sheet

Abstract. A new methodology for retrieval of glacier and ice sheet elevations and elevation changes from CryoSat-2 data is presented. Surface elevations and elevation changes determined using this approach show significant improvements over ESA's publicly available CryoSat-2 elevation product (L2 Baseline-B). The results are compared to near-coincident airborne laser altimetry from NASA's Operation IceBridge and seasonal height amplitudes from the Ice, Cloud, and Elevation Satellite (ICESat). Applying this methodology to CryoSat-2 data collected in interferometric synthetic aperture mode (SIN) over the high-relief regions of the Greenland Ice Sheet we find an improvement in the root-mean-square error (RMSE) of 27 and 40 % compared to ESA's L2 product in the derived elevation and elevation changes, respectively. In the interior part of the ice sheet, where CryoSat-2 operates in low-resolution mode (LRM), we find an improvement in the RMSE of 68 and 55 % in the derived elevation and elevation changes, respectively. There is also an 86 % improvement in the magnitude of the seasonal amplitudes when compared to amplitudes derived from ICESat data. These results indicate that the new methodology provides improved tracking of the snow/ice surface with lower sensitivity to changes in near-surface dielectric properties. To demonstrate the utility of the new processing methodology we produce elevations, elevation changes, and total volume changes from CryoSat-2 data for the Greenland Ice Sheet during the period January 2011 to January 2015. We find that the Greenland Ice Sheet decreased in volume at a rate of 289 ± 20 km3 a−1, with high interannual variability and spatial heterogeneity in rates of loss. This rate is 65 km3 a−1 more negative than rates determined from ESA's L2 product, highlighting the importance of CryoSat-2 processing methodologies.
Interleukin-2 family cytokines: potential for therapeutic immmunoregulation

IL-2 is a four-helix bundle cytokine that was initially identified as a T cell growth factor more than two decades ago. Since then, extensive investigations have led to the discovery of additional cytokines, including IL-4, IL-7, IL-9, IL-15 and IL-21, which display many similarities with IL-2 and have been grouped, together with the latter, as a distinct IL-2 cytokine family. These cytokines are all globular proteins that contain two sets of short-chain α-helical domains. They all play major roles in promoting and maintaining T lymphocyte populations, albeit in non-redundant and often complementary manners, whilst acting on other cell lineages as well. Most remarkably, their cell surface receptor complexes, which consist of two or three subunits, including a cytokine-specific private subunit, all use a shared subunit called the common γ chain (γc). This common subunit was shown to be mutated in X-linked severe combined immunodeficiency and to uniquely recruit the Janus kinase, Jak3. Accordingly, IL-2 family cytokines all utilise Jak3 in their mechanisms of intracellular signalling, together with more ubiquitous kinases. Owing to their prominent roles in lymphocyte development and homeostasis, IL-2 family cytokines have been the focus of much interest for the purpose of therapeutic applications. They may provide tools to bolster immune responses for the treatment of neoplastic diseases, viral infections and immunodeficiencies. Conversely, their blockade may help achieve immunosuppression for the treatment of transplant rejection, as well as inflammatory, autoimmune and allergic disorders. Here, the patent literature of the past four years pertaining to these important cytokines will be reviewed in the context of the current understanding of their biological significance.