Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequencing and analysis of the DNA genome of the temperate bacteriophage Aa[Phi]23 of "Actinobacillus actinomycetemcomitans"

The entire genomic sequence of the AaΦ23 bacteriophage is presented. Its size is 43,033 bp and it has an overall molar G+C content of 41mol%. 57 potential open reading frames (ORFs) were identified. A putative function could be assigned to 20 of the 57 ORFs, i.e. to 35% of them. While another 25 ORFs share homologies with hypothetical proteins present in several bacteria or bacteriophages, 12 seem to be specific for the phage AaΦ23. Based on the genetic organization of its genome, AaΦ23 shares extensive similarities with lambdoid bacteriophages. Most functions described for lambda are also found on the AaΦ23 genome. We identified potential ORFs coding for the integrase mediating recombination at the attachment sites; the generalized recombination proteins ninB and ninG; both C1 and Cro regulators of lysogeny; the replication proteins O and P; the antitermination protein Q; two components of the lytic system; structural components of the virion head, tail, baseplate and tail fibers and both subunits of the terminase enzyme involved in DNA packaging. The sequence of the phage attachment site (attP) is located 19 bp upstream of the gene coding for the integrase. The attL and attR of two lysogenic A. actinomycetemcomitans strains and the attB sites in two non-lysogenic strains were also identified. The common att core is 49 bp in length. No gene coding for a known virulence factor was detected on the AaΦ23 genome. However, a DNA adenine methylase was characterized that may be functionally expressed from the prophage. This protein is of particular interest because DNA adenine methylase enzymes are involved in the virulence of several bacterial pathogens such as Salmonella typhimurium, Yersinia pseudotuberculosis, and Vibrio cholerae. Still, presence of ORFs coding for proteins modulating the A. actinomycetemcomitans pathogenicity cannot be exclude as no putative function was assigned to 37 ORFs. Preliminary data on the putative lytic enzyme of AaΦ23 suggest that expression, even at low level, of the cloned lys gene is lethal for Escherichia coli cells. Location on the genetic map, amino acid sequence homologies and conservation of structural key residues strongly suggest that the integrase is coded by orf1. Preliminary data on the functional characterization were inconclusive. Delineation of the integration elements of AaΦ23 will allow the construction of an integration vector for A. actinomycetemcomitans.
A dynamical system model for the onset of collective behavior in social amoebae

Based upon the splendid experimental result of Gregor et al. 2010, we present a dynamical system model on the motion of individual amoebae. The dynamics of our model qualitatively agrees well with Gregor et al.'s experimental result on the development of collective behavior in social amoebae.
Evaluación de la estabilidad genética de vitroplantas de Rubus glaucus mediante marcadores moleculares (RAPD)

Se obtuvieron plantas de Rubus glaucus mediante regeneración in vitro de yemas con sales minerales de Murashige y Skoog (1962) suplementadas con tiamina 0,4 mg.1-1, cisteína 100 mg.1-1, mio-inositol 100 mg.1-1, ácido ascórbico 100 mg.1-1, sacarosa 30 mg.1-1 y phytagel 2,7 mg.1-1, y como reguladores de crecimiento bencil adenina (BA) 1,5 mg.1-1 y ácido giberélico 1,5 mg.1-1. Se evaluó la estabilidad genética de las plantas micropropagadas durante diferentes etapas del cultivo in vitro, mediante el uso de marcadores moleculares tipo RAPD. En total se obtuvieron dieciocho bandas que corresponden a 16,44 kb analizadas del genoma. Tres bandas resultaron polimórficas en algunas plantas del subcultivo F12 y en plantas en condiciones de vivero. El análisis de similitud reveló una alta homogeneidad de las plantas obtenidas por organogénesis a través de callo y de las plantas en los subcultivos F1,F15 Y P1, P13, Pv del proceso de multiplicación in vitro.
Weaning and growth of Anguilla australis glass eels and elvers

Anguilla australis glass eels proved to be resilient and present strong aquaculture potential. General husbandry techniques, anaesthesia and prophylactic treatments were established for glass eels caught along the South East Coast of Victoria. Growth rate was highly variable, both between and within groups. Growth was affected by the presence or absence of a preweaning diet, weaning diet, weaning period, temperature, but not by size or density. Water quality parameters were also measured.
Juglans regia L., phenotypic selection and assessment of genetic variation within a simulated seed orchard.

Noble hardwoods are very important for the Italian furniture industry. Since 1985, approximately 170,000 ha have been planted in Italy with noble hardwoods. Among them, about 50% of species are represented by walnuts. Walnut (Juglans regia L.), not native in Italy, has been the focus of a substantial research effort for breeding and improvement programmes. The priority has been to preserve the in situ genetic resource still existing after intensive felling. Phenotypes suitable for timber production showing important traits such as straight stem, nice branch architecture, dominance and adaptation (phenology) have needed to be developed and selected. In order to reach this goals, selection of valuable progenies and the evaluation of the interaction genotype x environment, methods based essentially on a multi-trait Selection Index, were developed. Studies have been undertaken also to measure the variation of phenological traits, more correlated to traits valuable for architecture; in addition, neutral markers were used to assess genetic variation among different intensities of the adopted selections. The individual genetic component was found to be higher than at the inter-population level. Results showed that a hypothetical seed orchard made with progenies selected by morphology, phenology and genetic traits could provide ma- terial with a good performance and supply a variability similar to larger populations as the total plantation or the pseudo-natural system chosen for comparison.
THE EFFECT OF DIFFERENT MANURES AND SYNTHETIC FERTILIZER ON BIOCHEMICAL AND ANTIMICROBIAL PROPERTIES OF MENTHA PIPERITA L

The study was designed to examine the effects of different manures (fish, pigeon and cow) and synthetic fertilizer (nitrogen) on some biochemical activities of Mentha piperita L. (mint, peppermint). Seventeen different phenolic constituents and 19 essential oils were determined in M. piperita samples. While caffeic, gallic, ferulic, protocatechuic, syringic, o-coumaric acids and rutin were detected as common phenolics; carvone, limonene and 1.8-cineol were identified as major essential oil components in all mints. Total phenolic compounds, ferric reducing antioxidant power and cupric (III) reducing capacity (CUPRAC) tests were used to evaluate antioxidant capacities of the mints. The highest total phenolic compound (4.8 mg gallic acid equivalents/100 g) and antioxidant capacity (971 mM Fe(II)/mg; 823 mM Trolox /100 g) were observed in mints fertilized with pigeon manure. Mint samples also had different antimicrobial activities against the studied microorganisms (eight bacteria and two fungi), especially Escherichia coli and Listeria monocytogenes. Practical Applications M. piperita L. has been widely used since early times and its botanical extracts were being employed to treat diseases. These extracts need to be investigated to understand how their properties are effected by different manures and fertilizers. So the findings of this research will enable M. piperita L. breeders to cultivate this plant with high biological activity.
Macroecological patterns in mammal abundances provide evidence that an apex predator shapes forest ecosystems by suppressing herbivore and mesopredator abundance

Apex predators often exert strong, top‐down effects on ecosystems, and their removal can result in the dramatic reorganization of ecosystems owing to herbivores and smaller predators becoming the dominant trophic‐regulating species. However, field studies designed to understand the influence that apex predators have on ecosystems are hampered by the large spatial and temporal scales required. Here, we use pre‐existing datasets to test predictions on the direct and indirect effects of apex predators on mammals and vegetation generated from trophic cascade theory and the mesopredator release hypothesis.
Histiocytic sarcoma with visceral spread resembling metastasizing poorly differentiated mast cell tumor in a 13 year old dog.

*Corresponding Author Selda Curtseit selda.curtseit@gmail.com We describe an unusual case of disseminated histiocytic sarcoma (DHS) in a 13-year-old spayed female mixed breed Cocker. It started as a periocular multifocal nodular dermatopathy, without any other clinical and hematological abnormalities. In the process of clarifying the diagnosis, first test performed was cytologic examination of the fine needle aspirate, which was highly suggestive of a cutaneous poorly differentiated multifocal mast cell tumor (MCT). Deteriorating health status led to the decision for euthanasia, followed by necropsy. Based on histopathology and immunohistochemical stain, a final diagnosis of disseminated histiocytic sarcoma was made.
Molecular Analysis of the 3'-Terminal Region of Lily Latent Carlavirus from Lilium lancitoium

The 3,000 nucleotides of 3'-terminal region of the genomic RNA of a new isolate of carlavirus from a Korean native lily (Lilum lancitoium) was cloned and its nucleotide sequences were determined. The coat protein (CP) gene of the virus showed 72.0% to 72.8% nucleotide sequence identities and 86.9% to 88.0% amino acid sequence identities with those of the four strains (two Korean, one Dutch, and one Japanese isolates) of lily symptomless virus (LSV). Interestingly, different amino acid sequences between the new isolate and LSV strains were located at the N-terminal region of the CP. Pairwise amino acid sequence comparison of the CP gene revealed sequence identities of 22.0% to 71.1% between the virus and other 9 carlavirus species. The 25 kDa and 12 kDa proteins genes of the virus share 30.7% to 76.3% and 31.1% to 85.8% amino acid sequence identities, respectively, with those of 8 other carlaviruses. The 16 kDa protein gene of the virus shares 16.7% to 72.9% amino acid sequence identities with that of 9 other carlaviruses. These data indicate that the virus, designated as lily latent virus (LiLV), is a distinct of the Carlavirus genus and distinguished from the known strains of LSV.
Comparative utilization of urea and fungal treated mustard straw by sheep.

The present study was conducted to detennine relative efficacy of urea and fungal treated mustard straw in maintaining adult sheep. Mustard straw (MS) treated with urea (UTMS) and fungus (FTMS) was fed ad lib. to ewes in G1 and (i) respectively, along with 200 g concentrate mixture/head/day. Urea treatment ofMS increased its CP content from 3.7 to 7.2% which further increased to 7.7% in FTMS. Hemicellulose and cellulose content decreased with proportionate increase in NDF and ADF in UTMS while the cell wall constituents further decreased in FTMS. Daily DMI in unit body weight or metabolic body size was higher (P<0.01) in FTMS fed animals. Digestibility of DM, NDF and ADF increased (P<0.01) and hemicellulose decreased (P<0.01) in OG2 compared to G1 Although nutritive value of the lest diets was similar, DE intake in metabolic body size was higher in G2 Both G1 and G2 were in positive N balance, however, per cent N retention was comparatively lower (13.2%). Feeding ofUTMS or FTMS along with 200 g concentrate maintained sheep, whereas treatment of MS with Coprinus fimetarius did not add advantage over the urea treated MS.
Fruit quality, bioactive compounds and antioxidant capacity of 6 Iranian peach cultivars

Knowledge of fruit biochemical properties is very important for perception ofproduct behavior during harvesting, transportation, packaging, storing and regenerationprograms. In this study, physicochemical properties of fruit in 6 Iranian peach cultivars:‘Tak-daneh’, ’Zoodras’, ‘Anjiri-ye-khouni’, ‘Haj-kazemi’, ‘Zaferani’ and ‘Kosari’ weredetermined. For evaluation of antioxidant capacity and its relation with total phenolicsand flavonoids, total antioxidant capacity [measured with 3 methods: ferric-reducingantioxidant potential (FRAP), 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2, 2-azinobis (3-ethylbenzothiazoline-6- sulfonic acid) radical scavenging assay (ABTS)] and totalphenolics and flavonoids in fruits extracts of aforementioned peach cultivars weremeasured and then, correlation of these parameters were evaluated. The highest °Brix anddry matter content among the studied cultivars corresponded to ‘Anjiri-ye-khouni’ andthe highest fruit humidity correlated to ’Zoodras’ and ‘Haj-kazemi’. The highest values ofvitamin C corresponded to ‘Anjiri-ye-khouni’ and ’Zoodras’ had the lowest vitamin C.Total ascorbic acid content was higher, then reported for other peach cultivars in the literature cited. Results revealed that ‘Anjiri-ye-khouni’ among the studied cultivars hadthe best antioxidant activity, flavonoid content and fruit quality attributes.
The identification of novel inorganic carbon sensitive enzymes

Adenylyl cyclase catalyses the formation of the second messenger adenosine-3’, 5’-monophosphate from adenosine triphosphate, and is involved in a number of diverse signalling pathways in eukaryotes and prokaryotes. Adenylyl cyclases are diverse in their structure and biochemistry, and have been grouped into six distinct Classes (I–VI). The Class III cyclase homology domain comprises the majority of prokaryotic and eukaryotic adenylyl cyclases, and has been further divided into 4 sub-Classes (a-d) based on active site polymorphisms. A number of Class IIIb adenylyl cyclases display elevated catalytic activity in the presence of inorganic carbon. Whether a response to inorganic carbon can be observed in enzymes which do not possess a Class IIIb cyclase homology domain remains to be established. Experiments were performed to investigate the response to inorganic carbon of a Class IIIa cyclase homology domain; mammalian transmembrane adenylyl cyclase. In vivo experiments demonstrated that the activity of mammalian transmembrane adenylyl cyclase was potentially regulated by inorganic carbon, and that this had a downstream effect on the cAMP response element binding protein. In vitro experiments performed on a transmembrane adenylyl cyclase demonstrated that the increase in activity in the presence of inorganic carbon occurred through an increase in kcat and increased metal affinity. Experiments were performed to test the response to inorganic carbon of several enzymes that share a structurally similar active site with the adenylyl cyclases; the polymerase I family of prokaryotic DNA polymerases, the polymerase β family of DNA polymerases, and the guanylyl cyclases. Initial in vitro experiments performed on T7 RNA polymerase demonstrated a response to inorganic carbon, however, it was discovered that this was likely due to a non-specific effect of pH. It was shown that inorganic carbon increased assay pH over time, and this warranted a re-design of the in vitro assay used to test the response of an enzyme to inorganic carbon. This new in vitro assay methodology was used to re-test T7 RNA polymerase, as well as test DNA polymerase β and several guanylyl cyclase, and demonstrated that these enzymes were non-responsive to inorganic carbon. Using this newly devised in vitro assay, experiments were performed to re-test the response of mammalian transmembrane adenylyl cyclase to inorganic carbon, and demonstrated that this enzyme was unlikely to be regulated by inorganic carbon. Furthermore, this new in vitro assay was used to re-test the response of several Class IIIb cyclase homology domains to inorganic carbon. Results demonstrated that mammalian soluble adenylyl cyclase was responsive to inorganic carbon, however, results provided evidence to suggest that two prokaryotic Class IIIb cyclase homology domains (CyaB1 from Anabaena PCC 7120 and CyaC from Spirulina platensis) were possibly non-responsive to inorganic carbon.
Dipetalogastin, a potent thrombin inhibitor from the blood‐sucking insectDipetalogaster maximus

A cDNA coding for the thrombin inhibitor dipetalogastin has been isolated from a stomach library of Dipetalogaster maximus, a blood-sucking insect. The open reading frame of the cloned inhibitor cDNA codes for a protein of 344 amino-acid residues. Sequence analysis reveals the existence of three repeated homologous main regions, indicating that the inhibitor consists of three domains. Each domain shows a double-headed structure with an internal sequence homology like rhodniin, the thrombin inhibitor from the blood-sucking insect Rhodnius prolixus. Peptide sequence comparisons of the deduced amino-acid sequence exhibit a high homology of the domains I and II to the natural inhibitor dipetalogastin from the stomach content of D. maximus and to rhodniin, respectively. Significant sequence similarities to Kazal-type inhibitors, like the conserved sequence CGXDXXTYXNXC and several cysteine residues, indicate that the thrombin inhibitor from D. maximus is a further blood-sucking insect which belongs to the Kazal-type family (besides rhodniin). A biologically active recombinant protein corresponding to domain II of the dipetalogastin cDNA was expressed in Escherichia coli. The isolated recombinant dipetalogastin with a molecular mass of 12.91 kDa has proved to be a specific thrombin inhibitor similar to its natural counterpart as well as rhodniin and hirudin. The Ki value of the recombinant dipetalogastin was determined to be 49.3 ± 22.28 fm.
Immunological studies on staphylococcal superantigen-like proteins.

The staphylococcal superantigen-like proteins (SSLs) are a family of polymorphic paralogs encoded within the Staphylococcus aureus genome, whose function remains unknown. The ability of SSL7, and a closely related paralog SSL9, to interact with cells of the immune system was investigated. Within the populations of human white blood cells, both SSLs interact selectively with monocytes, via specific but separate binding sites, leading to rapid uptake of SSLs. In addition, SSLs are rapidly taken up by dendritic cells (DC), but not macrophages, and target the mannose-receptor dependent endosomal antigen processing pathway. The effect of these proteins on the functional capacity of antigen presenting cells to uptake and present antigens to T cells was also determined. Neither SSL was toxic to DCs and the presence of SSL protein did not inhibit the antigen presenting cell activity, in terms of stimulation of either allogeneic or recall T cell responses. The immunological response to the SSL proteins in the normal human population was investigated. More than 30% of healthy normal subjects tested showed T cell responses to both SSL7 and SSL9. Moreover, almost all individuals had specific non- cross reacting antibodies against this family of proteins. In order to identify the SSL receptor(s), affinity chromatography techniques were used to isolate and identify the receptor(s) from selected cell lines. A single specific protein band that may represent the putative SSL receptor was observed, and mass spectrometry identified a candidate binding protein as heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa, GRP78 (BiP)). The presence of eleven members of this protein family within the pathogenicity island SaPIn2 in almost all S. aureus strains tested so far, suggest that these proteins have important non-redundant biological functions as agents of host/pathogen interactions. The data presented in this thesis further suggests that this function may involve targeting the host antigen presenting cell.
DOMINANCE RELATIONS IN POLISTES CANADENSIS (L.), A TROPICAL SOCIAL WASP

SUMMARY Most established colonies of Polistes canadensis canadensis (L.) (Hymenoptera Vespidae) observed in eastern Colombia (Meta) were dominated by despotic, territorial queens that actively suppressed aggressive behavior of nestmates via physical approach and attack. Dominance hierarchies, which require repeated interaction on the part of aggressive subordinates, were not observed in such colonies; however, a classic (PARDI, 1946) hierarchy formed on a nest lacking a despotic queen. Restricting the movements of a despotic queen to a limited region on the nest showed that physical contact or very near approach is necessary for queen control in this species: females that had remained off the nest prior to queen tethering began to frequent the egg-laying region of the nest out of reach of the tethered queen, and one established a territory there. Unmated females were unaggressive even when possessing developed ovaries and ovipositing on queenright nests; they exhibited surreptitious oviposition and worker.
Early Lessons in Implementing the Sustainable Development Goals in India: The Example of Assam

Assam has made vigorous efforts since 2015 towards achieving the Sustainable Development Goals (SDGs). Cognizant of the state’s weak progress in development, its recent governments – irrespective of political affiliation– adopted the SDGs and Assam became the first state in India to do so. The paper discusses in detail the steps taken so far which include developing an overall vision of an SDG-fulfilled Assam in 2030; preparing a comprehensive strategy in a participatory fashion to achieve that vision; and steps taken to implement and monitor the strategy. The Assam experience has many important lessons. These include the criticality of motivating staff at all levels to instill the SDGs in every aspect of their work and the role of leadership in this respect; proactively forging partnerships with all stakeholders including the legislature and the judiciary and creating an environment for such partnerships to flourish; the general need for adopting a result and outcome-based development process that the SDGs represent abandoning narrow departmental and output-based activity and practice. These would require initiating institutional and organizational changes including to ensure that major improvements take place in project implementation processes. Also essential is inculcating a culture of innovation –including technological innovation–in every sphere of public service; and developing effective coordinating mechanisms to ensure that all concerned stakeholders work synergistically to achieve the SDG outcomes. Also, very critical is the role of national and global partners in supporting Assam’s earnest efforts as the resource, knowledge and capacity gaps that Assam faces are too large for it to fill through its own means –even with its best efforts.