Miracle-dz/UniFAR-FTUs huggingface dataset:
Immune presentation and recognition of class I MHC phosphopeptide antigens

Alterations to metabolic pathways, in particular post-translational modification, are a recognised hallmark of diseases such as autoimmunity, inflammation and cancer, and potentially provide a source of altered self antigens that can stimulate immune responses. Most notably, phosphorylated peptides have emerged as a group of tumour associated antigens which can be presented by MHC molecules and recognised by T-cells, and therefore represent promising candidates for future cancer immunotherapy strategies. However, how antigen phosphorylation impacts upon antigen presentation and recognition remains unclear. During this study I demonstrated that the phosphate moiety of phosphopeptides bearing the canonical P4 phosphorylation is more structurally diverse in its binding mode than previously thought. Strikingly, two epitopes exhibited a major conformational change upon addition of the phosphate moiety, effectively creating “conformational neoantigens”. This occurred through a similar mechanism for each epitope, whereby the presence of the phosphate moiety raised the position of the P4 Serine, allowing phosphate-mediated contacts with MHC residues and distorting the conformation of the central epitope region most critical for T- cell receptor recognition. Finally, I found that recognition of phosphopeptides can be both phosphate-dependent and epitope-specific at the level of the T-cell receptor. Therefore, this study shows that phosphorylation can have a profound and diverse effect on antigen binding, epitope identity and T-cell receptor recognition. In summary, my studies suggest that phosphopeptides are not only tumour associated but also highly antigenically distinct, establishing them as attractive candidates for cancer immunotherapy strategies.
Comparative evaluation of the toxicity of lambda cyhalothrin and spinosad on the insect pests and auxiliary fauna in an orange orchard of the central Mitidja (Blidean Atlas, Algeria).

Impact of phytosanitary treatments on time variation in the abundance and diversity of the insect fauna was evaluated on an orange orchard in Central Mitidja. The ecotoxicity of Lambda-cyhalothrin and spinosad applied to the approved dose and half-dose were evaluated through the abundance and availability of pest populations and associated auxiliary procession after a period of 16 days exposure. Our results showed that Lambdacyhalothrin has a toxic effect on the aphid residual population during 12 days after treatment, which is moderately toxic from the 13th to the 16th day, while spinosad has a neutral effect during the hole exposure period. Community of the insect fauna harvested during the 16 days of observation after treatment consists of 12 species of phytophagous, 11 parasits and 13 predators. Under the effect of the approved dose of Lambdacyhalothrin, temporal fluctuation pest shows a slight increase in the first 12 days with a significant difference compared to control (23.30% in 12 days). The Aphididae, Phyllocnistis citrella and Ceratitis capitata are the most influenced unlike Coccidae, Aleurodidae and Tetranychus sp. The similarity analysis to one factor shows very highly significant differences between two types of treatments and between each treatment group and the controls. These differences may be due to variations in the relative abundance of different taxa or species composition of communities. Lowest contribution differences are recorded in parasitoïds and Chrysopidae.
Scale-dependent approaches inconservation biogeography of acosmopolitan raptor: the Osprey

Being a cosmopolitan and migratory species, the osprey Pandion haliaetus provides a good opportunity to explore how behavioural adaptations in different populations, that evolved under different ecological conditions and are widely spaced, can be the proximate causes of geographical distribution, genetic divergence, population connectivity, migratory strategies and foraging ecology. According to this, a multi-scale integrated approach has been adopted for the osprey: through an interdisciplinary framework made by molecular ecology, trophic ecology as assessed via stable isotopic analyses, spatial ecology through the use of novel biotelemetry tools, as well as population dynamics, fish censuses and assessments of levels of human disturbance, we: a) evidenced the existence of four different lineages at global scale that should be treated as Evolutionary Significant Units (ESUs) and deserve specific management; b) revealed population connectivity in the Western Palearctic; c) disentangled the migratory behaviour and winter ecology of Mediterranean ospreys and compared it with northern European populations, in an evolutionary context; d) stressed the need of adequate management measures to be adopted for three local populations of the Mediterranean basin (Corsica, Morocco and Italy). Overall, this work has led to some important advances with respect to the conservation biogeography of ospreys at different scales. Those insights are particularly valuable with respect to the effective management of this emblematic species.
Effect of photoperiod and feeding frequency on growth and feed utilization of fingerlings Persian sturgeon (Acipenser persicus)

The effects of photoperiod (12L:12D and 18L:6D) and feeding frequency (three, four and five evenly spaced daily feedings) of 10% biomass per day during light hours on growth and stress response of Persian sturgeon (Acipenser persicus) fingerlings were evaluated. The interaction between photoperiod and feeding frequency was not significant (P>0.05). Faster growth was observed in fish exposed to an 18L:6D photoperiod (P 0.05) and faster than when fed only three meals (P 0.05). Stress indicators (cortisol, glucose and haematocrit) did not differ between photoperiods (P<0.05). The results showed that 0.9–8.0 g Persian sturgeon fingerlings should be reared with an 18L:6D photoperiod and fed four times per day to obtain good growth and FCE.
Influence of Salix babylonica extract, exogenous enzyme of xylanase and their combination on blood haematological and biochemical profile in sheep and goats

The study was made to investigate effect of exogenous enzyme of xylanase, Salix babylonica extract and their combination on blood haematological and biochemical profile in lambs and goats. Suffolk lambs (4) and Saanen goats (4) were used in a Latin square design (4 animals × 4 treatments in 4 periods) for 15 days of adaptation. Animals were fed the basal diet plus 30 ml of water (control), or plus 30 ml of exogenous enzyme xylanase (EZ), or plus 30 ml of S. babylonica extract (SB), or plus 30 ml of xylanase + 30 ml of SB extract (EZSB). The daily dose of treatments was given orally before the morning feeding. Blood samples (5 ml) were collected on day 15 of each period and analyzed for haematological and biochemical profile. Treatments had affected hematocrit in lambs; eosinophils and glucose in goats. Since all the studied blood parameters were within the normal range for healthy goats and there were no signs of disease, it is concluded that xylanase, S. babylonica and their combination did not pose any threat to the health of the animals under the conditions of the experiment where both feed additives are innocuous.
Inheritance Pattern of Growth and Wood Traits in Teak (Tectona grandis L.f.).

Abstract Inheritance pattern of wood traits, especially heartwood/ sapwood percentage and specific gravity and interactions of wood traits with other growth traits were investigated in a 27-year-old half-sib progeny trial of teak. Wood traits showed highly significant variation for specific gravity, heartwood and sapwood percentage at family level. There was non-significant family vs. replication variation for these traits. Among the growth traits, there was significant variation for height and girth. Families and individual trees showed varying levels of heritability. Among the growth traits, height showed high heritability (individual tree heritability, h2 (i) = 34.3%; family heritability, h2 (f ) = 34.1%) followed by girth (h2 (i) = 19.4%; h2 (f ) = 31.4%). Among the wood traits, maximum heritability values were obtained for sapwood percentage (h2 (i) = 76.6%; h2 (f ) = 70.7%) and heartwood percentage (h2 (i) = 76.9%; h2 (f ) = 69.7%). Specific gravity exhibited heritability values of 29.1 and 41.8%, at individual tree and family level, respectively. Family heritability was higher than single-tree heritability for specific gravity; single-tree heritability exceeded family heritability for heartwood percentage. Specific gravity exhibited significant positive genotypic correlation with heartwood percentage suggesting that improvement in heartwood percentage would lead to a correlated improvement in specific gravity. Heartwood percentage showed significant positive correlation with growth traits viz., height and girth. Some of the families showed good GCA for growth and wood traits investigated. The good general combiners identified in the present study can be used for establishment of advanced generation seed orchards and breeding arboreta for improvement of teak for specific or combination of above traits.
Invitro complex‐formation between the molecular chaperone DnaK and staphylococcal ProteinA derivatives produced in Escherichia coli and its use inthe purification of DnaK

Complex‐formation between a truncated staphylococcal Protein A produced in Escherichia coli and a native E. coli molecular chaperone, DnaK, can be used for the purification of DnaK by IgG‐affinity chromatography. The half‐time constant for in vitro formation of the Protein AŐDnaK complex is about 14 min. Complex‐formation in the presence of ATP is faster, but pre‐incubation of DnaK with ATP decreases the final amount of the complex. A second complex with a slower migration on native PAGE is formed when the ratio of DnaK to Protein A is increased. A derivative of Protein A, ZZ, which essentially contains only two modified domains of Protein A, did not bind DnaK. After insertion of a tryptophan‐rich peptide close to the C‐terminus, the resulting protein, ZZT3, became able to bind DnaK. The binding of these three proteins to DnaK correlates with proteolysis in E. coli, indicating a possible role for the binding of DnaK in the control of proteolysis.
High Correlation between Alu Elements and the Conversion of 3' UTR of mRNAs Processed Pseudogenes

Even though it represents of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.
Feeding broiler chickens with practical diets containing lupin seeds (L. angustifolius or L. luteus): effects of incorporation level and mannanase supplementation on growth performance, digesta viscosity, microbial fermentation and gut morphology.

Total 208 day-old female broilers were fed on isonitrogenous and isoenergetic diets containing seeds of sweet narrow-leafed (L. angustifolius cv. Bojar - NL) or sweet yellow (L. luteus cv. Parys - YL) lupin at the level of 0 (control, C), 10% (days 1-14), and 15% or 25% (days 15-35 of life). The diets were fed unsupplemented or supplemented with mannanase. At the end of second week of life, the birds fed both lupin diets were smaller than control birds, due to lower feed intake (P < 0.05). The final body weight ( P < 0.05) and body weight gain (P < 0.01) in birds fed the NL were higher than in those fed the YL diets due to higher (P < 0.01) feed intake, but their feed conversion ratio was worse (P < 0.01). The higher dietary lupin level did not affect feed intake, but depressed feed utilization. The relative liver weight was greater in birds fed YL than NL. The viscosity of ileal digesta in birds fed the NL diets averaged 3.12 mPas.s and was significantly greater than in control and YL-fed birds. Villi height and crypt depth were lower (P < 0.05) at the increased level of di- etary lupin. The dietary treatments did not affect the total short-chain fatty acid concentration in ileal and caecal digesta. Mannanase supplementation did not significantly affect any of the measured parameters, but increased the butyrate concentration in caecal digesta (P < 0.05). Inclusion of sweet lupin at a 15% level can be accepted in older broiler diets provided with adequate amino acid and fat supplementation.
FOLIAGE YIELD, CHEMICAL COMPOSITION AND INTAKE CHARACTERISTICS OF THREE MUCUNA VARIETIES

The effect of variety and fertiliser on foliage yield and chemical composition of the foliage of three mucuna varieties, Mucuna deeringeana, Mucuna cochinchinensis and Mucuna spp. var, Ghana, was studied in an experiment in Burkina Faso in 2005 and 2007. The chemical composition and intake of hay from the same mucuna species were also studied using six Zebu cows per treatment offered 1/3 of their diet as grass hay. The experimental design of the agriculture experiment in both years was a randomised block with 3 mucuna varieties, not fertilised or fertilised with 2 kg DM/m2 of cow manure and with 4 replications. The foliages were harvested when 75% of the plants were flowering both for measuring foliage yield and for making hay. Soil characteristics before and after the experiment, dry matter yields and stem/leaf ratio of the vines were recorded and chemical composition of the foliages analysed. The mean age at harvesting was 57 d for M. spp. var. Ghana that was significantly shorter than for M. deeringeana (63 d) and M. cochinchinensis (81 d). Age at harvesting was not significantly affected by fertilisation. Dry matter yield was significantly lower for M. spp. var. Ghana, 1.71 t/ha for the unfertilised plots, compared to 3.29 and 3.07 t/ha for M. deeringeana and M. cochinchinensis, respectively. Fertilisation with manure more than doubled the yield for all varieties. There was no difference in stem/leaf ratio due to variety or fertiliser. The leaves+petiole fraction was generally heavier than the stem fraction. M. spp. var. Ghana had significantly higher content of crude protein than M. deeringeana and M. cochinchinensis (204, 177 and 150 g/kg DM, respectively). M. cochinchinensis had significantly higher ADF content than M. spp. var. Ghana, 474 and 369 g/kg DM, respectively. M. spp. var. Ghana had the highest CP content (209 g/kg DM), significantly different from M. cochinchinensis (165 g/kg DM) but not from M. deeringeana (192 g/kg DM). M. spp. var. Ghana had the best intake characteristics (4659 g and 3668 g/d for cows and heifers, respectively), but significantly so only for cows. In conclusion, the high foliage yield, the possibility of increasing soil fertility through N fixation and the high nutritive value of the foliage makes mucuna an interesting feed for ruminants even in areas with low soil fertility and a short rainy season.
Cadmium induced alterations in certain aspects of protein metabolism of the freshwater mussel, Lamellidens marginalis (Lamarck) and freshwater fish, Labeo rohita (Hamilton).

The levels of glutamine, ammonia and urea and the activities of alanine and aspertate aminotransferases (AlAT and AAT) and glutamate dehydrogenase (GDH) were estimated in the organs of mussel and fish exposed to acute concentration (7.0mg/l) of cadmium relative to their controls at day 1, 2 and 3. The AlAT and AAT activities decreased with an increase in GDH activity and glutamine levels in all the organs of the mussel and fish, greater in degree in fish than in mussel. The level of ammonia increased with a decrease in urea level in all the organs of mussel and fish. Eeither the increase or decrease in parameters was more in fish than in mussel and they were in the order day 1 < 2 > 3 in mussel and day 1 < 2 < 3 in fish over time of exposure. Among the organs, the degree in all the changes of all the parameters of protein metabolism were more or less insignificant and inconsistent but in general they were in the order ctenidium > mantle > hepatopancreas > foot in mussel and kidney > liver > gill > muscle in fish. In between the two animals, the degree of either the decrease or increase, as the case may be, in the parameters studied was more in the organs of fish and less in mussel. Further, the changes were progressive overtime of exposure in fish, but a slight recovery was observed at day 3 in mussel. The results indicated increased deamination, ammonia accumulation and suppression of urea synthesis in the organs of both the animal groups exposed to acute cadmium stress, with a greater in degree and progressive over time of exposure in fish.
Diverse responses of forest growth to drought time‐scales in the Northern Hemisphere

We thank all contributors and also the NOAA (ITRDB), CRU and the Spanish Meteorological State Agency (AEMET) for providing the data used in this study. This work has been supported by research projects CGL2011-27574-CO2-02, CGL2011-27536 and CGL2011-26654 financed by the Spanish Commission of Science and Technology and FEDER, projects 012/2008 and 387/2011 financed by Organismo Autonomo Parques Nacionales (Spain), project ‘Demonstration and validation of innovative methodology for regional climate change adaptation in the Mediterranean area (LIFE MEDACC)’ financed by the LIFE programme of the European Commission and Project CTTP1/12 financed by ‘Comunidad de Trabajo de los Pirineos’. C.A. -M. was supported by the grant JCI-2011-10263. The authors wish to acknowledge the editor and three anonymous referees for their detailed and helpful comments to the original manuscript.
A complete protocol for in situ hybridization of messenger RNAs in brain and other tissues with radi

A disposable flexible disc radial cuvette array has its cuvettes divided into inner compartments and outer compartments by a ramp-shaped wall. These cuvettes are separated from their adjacent cuvettes by dual side walls and have uniform parameters. The annular cuvette array includes an integral opaque horizontal annulus having a first radial series of slots thereon, substantially aligned with the radial centers of the outer ends of the cuvettes, and has a second radially spaced set of slots generally aligned with the side walls. The cuvette walls and array hub portion provide rigidity. The annulus also has an inwardly extending flange covering the outer radial ends of the cuvette, there being formed therein slots open to both the inner and outer compartments. Locating projections extend upwardly from the disc surface in an embodiment adapted to position a rotatable, cuvette numbering, annular ring, the ring being variably, rotatably positionable to provide selectivity of the cuvette numbers. The thickness of the plastic material forming the array is selected empirically for proper optical and strength characteristics. The array is flexible and integrally spring biased between hub and annulus to maintain the bottom walls of the cuvettes against the rotatable support with which the cuvette array is to be utilized under pressure to maximize contact therebetween. The annulus is fusion bonded to the hub and cuvette chamber portion to form the integral array.
Relationship between genetic distance and heterosis under different fertilizer applications in rice.

in the female reaction, but by a dominant gene(s) in the male reaction. The growth of pollen tubes was investigated to examine F2 segregation. The female and male reactions in each plant were estimated by crossing to IR58 and with Akihikari, respectively (Fig. 1). The result showed that the female and male reactions seemed to be independently inherited, suggesting that the gene(s) controlling the female and male reactions could be recombined.
Munias and Mannikins

Munias are widespread throughout the Old World's tropical regions. In their natural habitat, they are birds of the savanna, but they have adapted to a number of different habitats, including areas inhabited by humans. They range in size from the Java sparrow (which is about the size of a common starling) to the diminutive Madagascar mannikin. Their striking plumage makes them popular as cagebirds and they breed readily in captivity. This book covers 43 species of munias and mannikins. The author has recently described one new species and ten new subspecies to science.
FUSARIUM HEAD BLIGHT: WINTER WHEAT CULTIVAR RESPONSES AND CHARACTERIZATION OF PATHOGEN ISOLATES

Fusarium head blight (FHB) is a destructive disease of wheat (Triticum aestivum L). FHB reduces yield and grain quality and causes accumulation of the mycotoxin deoxynivalenol (DON) in grain. Cultivar resistance is one of the most effective management strategies for FHB. Experiments were conducted to 1) identify winter wheat cultivars with resistance to FHB and DON accumulation, 2) determine the effect of winter wheat cultivar on the relationship between FHB and DON concentration, and 3) identify the major species of Fusarium causing FHB in Nebraska and characterize its isolates. Differences (P ≤ 0.05) were detected among cultivars in FHB index, Fusarium-and Overland were moderately resistant to FHB and DON accumulation. Harry was resistant to FHB but susceptible to DON accumulation. Overley, Jagalene, Wesley, and 2137 were susceptible to FHB and DON accumulation. The relationship between FHB severity and DON concentration was linear and positive regardless of cultivar. However, regression slopes indicated that this relationship was cultivar dependent. Forty of 41 isolates of Fusarium obtained from infected winter wheat kernels in grain collected from elevators and fields in Nebraska were identified by polymerase chain reaction (PCR) morphological characteristics as Fusarium graminearum Schwabe (Teleomorph: Gibberella zeae (Schwein.) Petch). Seventeen selected isolates differed (P ≤ 0.05) in the number and size of perithecial units (single perithecium or clusters of perithecia) produced in culture and seven selected isolates differed (P ≤ 0.05) in aggressiveness on wheat spikes and detached leaves. Based on aggressiveness on wheat spikes, the seven isolates were grouped into three categories: 1) highly aggressive (isolates 103, 110, and 119), 2) moderately aggressive (isolates 91 and 98), and 3) weakly aggressive (isolates 90 and 97). iv To my parents, Rogelio and Lolis, for their lessons and wisdom. To my brothers, Joaquin and Edgar, for their friendship. To my aunt Anadelia, for my first book. v ACKNOWLEDGMENTS First at all, I would like to express my most sincere gratitude to my advisor, Dr. Stephen N. Wegulo, for accepting me in his lab and for giving me the opportunity to develop myself intellectually, academically, and spiritually. Thank you for your trust, help, support, guidance and encouragement. Your passion and hard work as a scientist have truly changed my perspective of science and my life. I was privileged, because few people have the opportunity of working with persons as you, with the highest quality as researcher, as human being, and as a person. For all …