Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting cancer vulnerabilities through gene networks under purifying selection in 4,700 cancer genomes

Large-scale cancer sequencing studies have uncovered dozens of mutations critical to cancer initiation and progression. However, a significant proportion of genes linked to tumor propagation remain hidden, often due to noise in sequencing data confounding low frequency alterations. Further, genes in networks under purifying selection (NPS), or those that are mutated in cancers less frequently than would be expected by chance, may play crucial roles in sustaining cancers but have largely been overlooked. We describe here a statistical framework that identifies genes that have a first order protein interaction network significantly depleted for mutations, to elucidate key genetic contributors to cancers. Not reliant on and thus, unbiased by, the gene of interest’s mutation rate, our approach has identified 685 putative genes linked to cancer development. Comparative analysis indicates statistically significant enrichment of NPS genes in previously validated cancer vulnerability gene sets, while further identifying novel cancer-specific candidate gene targets. As more tumor genomes are sequenced, integrating systems level mutation data through this network approach should become increasingly useful in pinpointing gene targets for cancer diagnosis and treatment.
A fluorogenic nanobody array tag for prolonged single molecule imaging in live cells

Prolonged single molecule imaging in live cells requires labels that do not aggregate, have high contrast, and are photo-stable. To address these requirements, we have generated arrays of modular protein domains that function as fluorophore recruitment platforms. ArrayG, a linear repeat of GFP-nanobodies, recruits free monomeric wild-type GFP, which brightens ~15-fold upon binding the array. The fluorogenic ArrayG tag effectively eliminates background fluorescence from free binders, a major impediment to high-throughput acquisition of long trajectories in recruitment based imaging strategies. The photo-stability of ArrayG and consistently low background made it possible to continuously track single integrins for as long as 105 seconds (2100 frames). Prolonged tracking of both kinesin and integrin revealed repeated state-switching events, a measurement capability that is crucial to a mechanistic understanding of complex cellular processes. We also report an orthogonal array tag, based on a DHFR-nanobody, for prolonged dual color imaging of single molecules.
Use biofertilizer of agronomic performance cultivars Allium ascalonicum in edafoclimatic conditions of the Brejo Paraibano-Brazil

Allium ascalonicum originate from the Mediterranean, aliácea of great economic importance, due to its wide acceptance by the market characteristics as soft, sweet and pleasant taste. Currently it has expanded organic agriculture the cultivation of these species, with the use of organic fertilizer, which is responsible for development of the plant increasing productivity. Therefore, this study aimed to evaluate the use biofertilizer of agronomic performance cultivars A. ascalonicum in edafoclimatic conditions of the Brejo Paraibano-Brazil. The experiment was carried out on farmer Pitiá Areia-Paraiba-Brazil, which was soil preparation done, incorporated 30 kg ha of manure, then sowing onions Shallot White and Brown plat spacing 0,20 x 0,10 m. After 15 days of cultivation the biofertilizer was applied (50% fresh manure and 50% water) at doses 0,0 and 3,0% in leaves of A. ascalonicum. Harvest was done to seventy after planting days, the fruits were transported to Seed Technology Laboratory at CCA/UFPB-Areia-Paraiba/Brazil, where the following evaluations were performed: bulb diameter, bulbils number per bulb, average bulb weight, dry matter bulb and productivity. The experimental design was completely randomized with four treatments (two biofertilizer doses of 0,0 and 3,0%), (two varieties Shallots White and Brown) and four replications. The data submitted to ANOVA, means were compared by Tukey test at 5%, SISVAR. The biofertilizer doses did not influence the evaluated characteristics, except dose of 3,0% that favored increased productivity of onions Shallots White and Brown. Key-words: Shallot, Organic system, Productivity
Dynamics of Prunus Necrotic Ringspot and Apple Mosaic Ilarviruses in Stone Fruits - A Serological Perspective

Prunus necrotic ringspot virus (PNRSV) and apple mosaic virus (ApMV) are common and widespread in different stone fruits causing crop losses (Scott, 2014; Pallas et al., 2012). In India, little is known on virus diseases of stone fruit trees and records are limited on the occasional finding of ilarviruses (PNRSV and ApMV) in major stone fruits grown in India (Kapoor and Handa, 2017a; Chandel et al., 2013). Studies on the deleterious effects on the growth and yield by both viruses on various Prunus hosts have been published by a number of authors (Kapoor and Handa, 2017b; Caglayan and Gazel, 1998; Alhudaib and Rezk, 2011). Besides stone fruits, the importance of ilarviruses in apple production system has been critically revealed by (Kapoor et al., 2018). Although, ilarviruses are latent in nature, visual symptoms caused by these viruses in the peach, plum and apricots are very similar and it is difficult to differentiate the two viruses in these hosts. PNRSV and International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 05 (2018) Journal homepage: http://www.ijcmas. com
Estimating Optimal Lysogenic Propensity for Viruses in Stressed Environments

Having infected a bacterial cell, a temperate phage has to make a choice between (a) integrating itself into the bacterial genome, i.e. lysogeny, and (b) using the bacterial machinery to create multiple copies of itself and lysing the cell in the process, i.e. lysis. In order to maximize its long-term growth rate, phages need to ensure that they do not wipe off their bacterial hosts. Temperate phages have been observed to exhibit lysogenic propensities dependent on the MoI (Multiplicity of Infection), among other factors. We propose a model to estimate the propensity of lysogeny opted for by the phages in order to maximize coexistence. One possible approach to do so is to adopt a strategy that would help to attain and maintain an approximately equal proportion of phages with respect to their host. We find that the optimal fraction of phages opting for lysogeny follows a sigmoidal relationship with the MoI and is comparable to results obtained experimentally. We further assess the impact of phage and bacterial environmental stresses on the lysogenic propensity. Our results indicate that the optimal value of lysogenic propensity is greatly dependent on the intensity of these stresses.
The rapid evolution of alternative splicing in plants

Alternative pre-mRNA splicing (AS) is prevalent among all plants and is involved in many interactions with environmental stresses. However, the evolutionary patterns and underlying mechanisms of AS in plants remain unclear. By analyzing the transcriptomes of six plant species, we revealed that AS diverged rapidly among closely related species, largely due to the gains and losses of AS events among orthologous genes. Furthermore, AS that generates transcripts containing premature termination codons (PTC), although only representing a small fraction of the total AS, are more conserved than those that generate non-PTC containing transcripts, suggesting that AS coupled with nonsense-mediated decay (NMD) might play an important role in regulating mRNA levels post-transcriptionally. With a machine learning approach we analyzed the key determinants of AS to understand the mechanisms underlying its rapid divergence. Among the studied species, the presence/absence of alternative splicing site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5’ donor site and 3’acceptor site, suggesting a relatively conserved AS mechanism. Comparative analysis further demonstrated that variations of the identified AS determinants, mostly are located in introns, significantly contributed to the AS turnover among closely related species in both Solanaceae and Brassicaceae taxa. These new mechanistic insights into the evolution of AS in plants highlight the importance of post-transcriptional regulation in mediating plant-environment interactions. One sentence summary Changes of intron located splicing regulators contributed to the rapid evolution of alternative splicing in plants.
Evaluation of various herbicides for controlling grassy weeds in wheat

A field study was carried out to evaluate the efficacy of various herbicides for controlling grassy weeds in wheat crop during winter 2011-12 at Adaptive Research Farm, Sheikhupura, Pakistan. Four herbicides viz. pinoxaden/cloquintocet-mexyl (Axial 100 EC) @ 825 mL ha -1 , clodinafop (Topik 15 WG) @ 300 g ha -1 , fenoxaprop-p-ethyl (Puma Super 75 EW) @ 1250 mL ha -1 , Iodo + mesosulfuron (Atlantis 3.6% WG) @ 400 g ha -1 were used. A weedy check was also maintained for comparison. All the herbicides decreased total weed population and their biomass as compared to weedy check. Axial 100 EC @ 825 mL ha -1 was found to be the most effective in reducing weeds population as well as weed biomass with maximum mortality. Axial herbicide reduced total weed density and total weed dry weight over control by 88% and 87%, respectively. This herbicide increased grain yield of wheat by 42% and also increased tillers per unit area, spike length, number of grains per spike, 1000-grain weight over weedy check control. The economic analysis showed that Axial herbicide gave the highest net benefits of Rs. 78200 ha -1 . The application of Topik herbicide gave maximum marginal rate of return (1056%) followed by spray of Axial herbicide which resulted in 877% MRR.
Spatial and Temporal Variation in Triglyceride Concentration in the Blood of Nestling Blue Tits Cyanistes Caeruleus

Plasma biochemistry values are useful tools for ecophysiological research of birds and other vertebrates. They provide data on the physiological and nutritional state of individuals in various life stages. We predicted that blood triglyceride levels correlate with nutritional state of birds and that this trait is temporally variable. Therefore, we studied the effects of year and distinct habitat type (urban parkland vs woodland) on triglyceride concentration in the blood of nestling Blue Tits Cyanistes caeruleus. We ascertained both seasonal and inter-habitat variation within the trait. Specifically, (1) nestlings from trophic rich forest site were characterised with significantly higher mean triglyceride levels, and (2) mean triglyceride content was significantly higher in one out of three breeding seasons. These results suggest that the studied trait may be used as a robust indicator of habitat trophic abundance and quality.
Plant Belowground Diversity and Species Segregation by Depth in a Semi-Arid Grassland

ABSTRACT Understanding the relationships between below- and aboveground plant community diversity and composition is essential for understanding plant-soil linkages and feedbacks. Here we examine the patterns of belowground plant species richness, evenness, community composition, and individual species relative abundance with soil depth in a rough fescue grassland. Plant taxa belowground were identified via next-generation sequencing of the trnL intron. We found weak positive below-aboveground concordance in plant species composition demonstrating a general similarity between aboveground and belowground communities. The positive relationship between below- and aboveground plant species richness was stronger within the A horizon than in the B horizon, indicating that some species avoided rootingmore deeply in the soil. For the most common graminoid species at the site, there was no evidence for depth-related rooting preferences for species of Carex (sedges) or Elymus (wheatgrasses), while the dominant native grass Festuca hallii preferentially rooted shallowly while the invasive grass Bromus inermis rooted more deeply. Differential rooting patterns among some of the dominant species suggests some degree of belowground niche differentiation may be important in structuring this plant community.
CHEMICAL, NUTRITIONAL AND ANTI-NUTRITIONAL COMPOSITIONS OF NEPHROLEPIS EXALTATA (L.) SCHOTT. (NEPHROLEPIDACEAE)

Chemical, nutrient and anti- nutrient compositions, elemental analysis and toxicity potentials of bipinnate and unipinnate leaflets of Nephrolepis exaltata were determined, evaluated separately and compared the nutritious potentials between the two types of leaflets statistically. Fresh, healthy, matured leaflets were collected from the two frond types, washed, air dried in the laboratory, ground and analyzed for proximate analysis, elemental compositions, dry matter, ascorbic acid, oxalate, phytate and cyanide contents in triplicate. The results of the proximate analysis showed protein (9.45±0.21, 12.47±0.08%), crude fibre (0.57±0.32, 0.47±0.30%), fat (0.47±0.40, 0.54±0.41%), ash (0.87±0.02, 0.93±0.11%), moisture (82.65±0.04, 78.50±0.05%), carbohydrate (5.98±0.16, 7.08±0.18%); dry matter (17.53±0.51, 21.50±0.72 g/100 g) and ascorbic acid (52.80±0.89, 69.96±0.01 mg/100 g) of bipinnate and unipinnate leaflets respectively. The result showed that the leaflets contains mineral elements such as potassium, sodium, calcium, iron, zinc, cadmium, lead, magnesium, manganese, copper, chromium and nickel; cyanide (0.12, 0.53) mg/100 g, oxalate (0.02, 0.02 mg/100 g) but phytate and arsenium were not detected from both bipinnate and unipinnate leaflets respectively. The cyanide and oxalate contents of both leaflets are very low and fall within the safe and acceptable limits as recommended by World Health Organization. Thus, they are potential good sources of dietary energy, protein, ascorbic acid and mineral contents in livestock diet. Unipinnate leaflets have significantly higher values (p lessthan 0.05) in most of the nutrients, therefore it is more nutritious. Keywords: Leaflets, livestock feed, Nephrolepis exaltata, proximate analysis, toxicants
Illegal trade of the Psittacidae in Venezuela

Abstract Illegal wildlife trade is one of the major threats to Neotropical psittacids, with nearly 28% of species targeted for the illegal pet trade. We analysed the most comprehensive data set on illegal wildlife trade currently available for Venezuela, from various sources, to provide a quantitative assessment of the magnitude, scope and detectability of the trade in psittacids at the national level. We calculated a specific offer index (SO) based on the frequency of which each species was offered for sale. Forty-seven species of psittacids were traded in Venezuela during 1981–2015, of which 17 were non-native. At least 641,675 individuals were traded, with an overall extraction rate of 18,334 individuals per year (35 years of accumulated reports). Amazona ochrocephala was the most frequently detected species (SO = 3.603), with the highest extraction rate (10,544 individuals per year), followed by Eupsittula pertinax (SO = 1.357) and Amazona amazonica (SO = 1.073). Amazona barbadensis, Ara ararauna and Ara chloropterus were the fourth most frequently detected species (SO = 0.564–0.615). Eleven species were involved principally in domestic trade (> 60% of records). Our approach could be the first step in developing a national monitoring programme to inform national policy on the trade in psittacids. Patterns and numbers provided may be used to update the official list of threatened species, and could also be used in planning conservation actions.
Meiofauna distribution on hard substrata in a submarine cave

For the first time the meiofauna of the rocky walls of a submarine cave was studied. The cave, known as il Ciolo (Strait of Otranto, south-east Italy) is a closed tunnel about 125 m long, with a maximum depth of 6 m below sea level. The meiofauna was collected from artificial panels and natural rocky walls. This double approach enabled: (1) the description of the community's initial organization (on artificial substrata), and (2), especially for Harpacticoida, its mature composition (on rocky walls), which also helped to establish spatial differences. The collected samples yielded 70 taxa in total. Harpacticoida represented the most important group of organisms in terms of both abundance and identified taxa. The meiofauna assemblage appeared not to be affected by community age, with the exception of the very early stage. The meiofauna of the cave showed assemblage differences from the entrance to the innermost positions, but not as evident as in the case of the macrobenthos. The similarity of community composition at different ages (6, 12 and 24 months) and at different positions along the cave could be the consequence of the specimens’ vagility.
Nuclear ERK Translocation is Mediated by Protein Kinase CK2 and Accelerated by Autophosphorylation.

BACKGROUND/AIMS The extracellular signal-regulated kinases (ERK) 1 and 2 (ERK1/2) are members of the mitogen-activated protein kinase (MAPK) family. Upon stimulation, these kinases translocate from the cytoplasm to the nucleus, where they induce physiological processes such as proliferation and differentiation. The mechanism of translocation of this kinase involves phosphorylation of two Ser residues within a nuclear translocation signal (NTS), which allows binding to importin7 and a subsequent penetration via nuclear pores. However, the regulation of this process and the protein kinases involved are not yet clear. METHODS To answer this point we developed specific anti phospho-SPS antibody, used this and other antibodies in Western blots and crystalized the phospho-mimetic mutated ERK. RESULTS Here we show that the phosphorylation of both Ser residues is mediated mainly by casein kinase 2 (CK2) and that active ERK may assist in the phosphorylation of the N-terminal Ser. We also demonstrate that the phosphorylation is dependent on the release of ERK from cytoplasmic anchoring proteins. Crystal structure of the phosphomimetic ERK revealed that the NTS phosphorylation creates an acidic patch in ERK. Our model is that in resting cells ERK is bound to cytoplasmic anchors, which prevent its NTS phosphorylation. Upon stimulation, phosphorylation of the ERK TEY domain releases ERK and allows phosphorylation of its NTS by CK2 and active ERK to generate a negatively charged patch in ERK, binding to importin 7 and nuclear translocation. CONCLUSION These results provide an important role of CK2 in regulating nuclear ERK activities.
Some toxicological impacts and invitro antibacterial activity of Datura innoxia extract in rats

The study was carried out to investigate some toxicological effects and in-vitro antibacterial activity of Datura innoxia dried leaves.The yield percentage of Datura innoxia 95% ethyl alcohol leaves extract was 19%. Phytochemicals analysis of both Datura innoxia leaves powder and alcoholic extract, indicated the presence of alkaloids, phenols, glycosides, tannins, resins, saponins, flavonoids and steroids which are responsible for toxic and therapeutic effects. The acute toxicological effect of Datura innoxia ethanolic extract in male rats was determined by estimation the oral median lethal dose (LD50) by up and down method was 1214 mg/kg. BW. The in-vitro antibacterial activity of Datura innoxia ethanolic extract and its minimum inhibitory concentration activity (MIC) showed that E. coli was more sensitive to D.I ethanolic extract than Staph. aureus, the MIC for D.I extract against E. coli was less than MIC against Staph. aureus which was 5 and 10 mg/ml respectively, also E. coli was more sensitive to ciprofloxacin .
Description and Characterisation of a Novel Model of Persistent Infection with Streptococcus Pneumoniae in the Lower Airways of Mice

This thesis reports the development of a murine model of low-level, long-term colonisation of the lower respiratory tract with S. pneumoniae, which would mimic the bacterial colonisation observed in COPD and severe asthma in humans. For a successful model of persistent infection, viable pneumococci would be recovered from the lower respiratory tract for a minimum of 28 days, mice would be asymptomatic but there would be an inflammatory response. After a single intranasal challenge of S. pneumoniae strain LgSt215, CBA/Ca mice had recoverable numbers of viable pneumococci in the lower airways for at least 28 days post-infection, with an accompanying inflammatory response that consisted of a transient neutrophilia but progressed to being predominantly monocytic with foci of fibroplasia at the transitional airways from 14 days post-infection. The next stage was to combine the new model of persistent pneumococcal infection with models that mimic other pathologies observed in COPD and asthma. Consequently an acute model of lipopolysaccharide-induced lung injury was combined with the model of persistent infection. This resulted in an increase in the number of neutrophils in the lower airways. However when the persistent pneumococcal infection model was combined with a model of ovalbumin-induced eosinophilic inflammation, the number of eosinophils induced was reduced, suggesting that the inflammatory response was no longer one of allergy, but mediated primarily by a Th1-mediated immune response. The observed phenotype mimicked the non-eosinophilic phenotype observed in half of mildto-moderate asthmatics. A new NADPH oxidase 4 inhibitor was tested in this combined model of inflammation, and it was seen that after administration of this inhibitor an improvement in ciliary function was observed. This model of persistent infection is an ideal tool to test hypotheses of triggers of exacerbation and for study of the role that bacterial infection play in the progression of COPD and asthma.
Chromosome banding in the genus Pinus V. Fluorescent banding patterns in 16 diploxylon pines

A BSTRACT: In Pinus , Subgenus Pinus 16 species were investigated on their somatic chromosomes by a fluorescent banding technique using chromomycin A 3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI). The chromosome number of 2 n =24 was commonly counted in all the species studied. Their karyotypes were composed of many long metacentric chromosomes and a few short submetacentric chromosomes, and two karyotypes were recognized in respect to number of short chromosomes in the subgenus. CMA-bands appeared at an interstitial and/or proximal region of chromosomes and DAPI-band did at a proximal region. Thin DAPI-bands appeared at interstitial regions and DAPI-dots appeared at a centromeric region in most chromosomes. In a chromosome complement each homologous chromosome was identified on the base of its shape and fluorescent banding pattern. The typical banding patterns were compared among the species studied. Many interstitial CMA-bands at the secondary constrictions appeared on many metacentric chromosomes. Proximal fluorescent bands varied in fluorescent nature and number and divided into several groups. Section Pinus short three chromosome pairs were two or three patterns of fluorescent banding. The section Trifolae species had many proximal DAPI-bands and less proximal CMA-bands than section Pinus . The shortest chromosome had proximal bands indicating two groups on the kinds of fluorescent band.