Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Habitat on Breeding Success in a Declining Migrant Songbird: the Case of Pied Flycatcher Ficedula hypoleuca

Abstract. Habitat is a key determinant of breeding success in hole-nesting birds. Identifying the factors that influence breeding success is important in understanding nest-site selection behaviour and devising appropriate conservation strategies. This is especially true for declining species like the migratory Pied Flycatcher Ficedula hypoleuca. Here, I analyse the effect of 24 habitat variables on clutch size, hatching success and fledging success for 137 Pied Flycatcher nests in Gloucestershire, UK, using volunteer-collected data from a 5-year period. More successful nests tended to be located in areas with a lower density of mature trees but abundant saplings. Tree and sapling species richness was also important. Success was positively related to abundance of Oak Quercus robur and Silver Birch Betula pendula and negatively related to Beech Fagus sylvatica, Sycamore Acer pseudoplatanus and Bracken Pteridium aquilinum. Success was lower in boxes facing south-southwest and higher in boxes located on sorter trees. Despite Pied Flycatchers often being regarded as birds of grazed (open) woodland, success was not related directly to grazing. Close proximity to footpaths was associated with significantly lower clutch size, numbers of young to fledge, and percentage success, while close proximity to water was associated with increased success at all stages of breeding. This is a single-site study and the generality of these findings at other sites cannot be assumed without empirical testing. However, the results provide useful additional insight into success-habitat interactions in this species that, to some extent, challenge the general view of Pied Flycatchers, in the UK at least, as grazed woodland specialists.
Mechanisms by which lumpy skin disease virus is shed in semen of artificially infected bulls

Lumpy skin disease (LSD) is a disease of significant economic importance in Africa. It causes considerable production losses and its presence in semen is a constraint to international trade. Recent findings that LSDV viral DNA can be found in the semen of artificially infected bulls for up to five months, while viable virus could be isolated 42 days after infection, indicated the need for studies into the mechanism by which this protracted shedding occurs. Six healthy, seronegative, postpubertal Dexter bulls were housed in vector-free stables and challenged with LSD virus by intravenous injection. Sheath washes, vesicular fluid and semen collection was performed every other day and subjected to PCR. On these days, blood was collected for serum neutralization tests and virus isolation, and ultrasonography of the reproductive tracts performed. Semen was centrifuged to separate cell-rich and seminal plasma fractions, and tested by PCR. Clinical parameters were recorded twice daily. Bulls shedding viral DNA 28 days after challenge were slaughtered, their reproductive tracts were harvested and diagnostic post mortem was performed. Histopathology, immunoperoxidase staining, electron microscopy, virus isolation and PCR were done on tissue samples. Of the six bulls, two showed no clinical signs, two showed mild and two showed severe clinical signs. Fever appeared five to seven days and lesions eight to ten days post challenge. Bulls were viraemic and febrile during the same time. Viral DNA was detected in all semen fractions of all bulls, but mostly from the cell-rich fraction and from the bulls showing the most severe clinical signs. Ultrasonography showed infarction in the testes and epididymides of the two bulls that were most severely affected. Necropsy of the two bulls that were still shedding after 28 days showed testicular degeneration and infarction, as well as epididymal granuloma formation. None of the accessory sex organs showed significant pathology. Histopathological changes seen were necrogranulomata in testes and peididymides. IMP staining of reproductive tissues showed that staining was restricted to areas in the testes and epididymides that were associated with necrosis. Virus could be seen on negative staining EM of sections of the testes. Our results show that LSDV is not limited to specific fractions of the ejaculate and that the testes and epididymides are most profoundly affected. Blood contamination is not responsible for the presence of viral DNA in semen, and it is unlikely that the virus is sperm-associated. Results suggest that the ejaculate is contaminated with viral DNA as it is shed from necrotic lesions in the genital tract. Further research is indicated into the ability of infected semen to produce disease as well as treatment protocols that could render semen free of viral DNA.
Madurez sexual, Índice de condición y rendimiento de Pinctada mazatlanica (Pterioida: Pteriidae), Golfo de Nicoya, Costa Rica

Se determino el indice de condicion, rendimiento y madurez gonadal de Pinctada mazatlanica (Hanley 1856), en Isla Pan de Azucar.Golfode Nicoya, entre setiembre de 1993 Y setiembre de 1994. El rendimiento en carne promedio fue de 13.89 ± 3.70 %, con un ambito entre 29.1 % y 14.13 % y el indice de condicion promedio fue de 18.92 ± 4.4 %, con un ambito entre 10.77 % Y 28.26 %. Durante todo el afio se encuentran individuos maduros, con dos picos de desove maximo en octubre 1993 y junio 1994.
Reading and engineering N-linked protein glycosilation in Escherichia coli

A number of proteobacteria carry the genetic information to perform N-linked glycosylation, but only the protein glycosylation (pgl) pathway of Campylobacter jejuni has been studied to date. Here, we report that the pgl gene cluster of Campylobacter lari encodes for a functional glycosylation machinery that can be reconstituted in Escherichia coli. We determined that the N-glycan produced in this system consisted of a linear hexasaccharide. We found that the oligosaccharyltransferase of C. lari conserved a predominant specificity for the primary sequence D/E-X-1-N-X+1-S/T (where X-1 and X+1 can be any amino acid but proline). At the same time, we observed that this enzyme exhibited a relaxed specificity towards the acceptor site, and modified asparagine residues of a protein at the sequences DANSG and NNNST. Moreover, C. lari pgl glycosylated a native protein of E. coli, demonstrating that the pgl machineries are general glycosylation systems with different efficiencies. Bacterial Nglycosylation appears as a useful tool to establish a molecular description of how singlesubunit oligosaccharyltransferases perform selection of glycosyl acceptor sites. Introduction N-Linked glycosylation is a ubiquitous protein modification that involves the decoration of selected asparagine residues within the sequences N-X+1-S/T (X+1≠P) with an oligosaccharide. This process is organized in a topologically equivalent way in eukaryotes and in prokaryotes (Yurist-Doutsch et al., 2008), and involves assembly of the glycan donor on a lipid anchor at the cytoplasmic side of the ER or of the plasma membrane, reorientation to the opposite face of the membrane, and subsequent attachment to the acceptor protein (Burda et al., 1999). The defining event of N-glycosylation is the formation of the Nglycosidic bond between the oligosaccharide and the asparagine side chain of the acceptor protein. This reaction is catalyzed by the oligosaccharyltransferase (OST), a single subunit enzyme in bacteria, archaea and protozoa, but consisting of a multimeric complex in other eukaryotes (Kelleher et al., 2006). The Stt3 protein represents the central component of the OST complex, and it is believed to be the catalytic subunit (Feldman et al., 2005, Igura et al., 2008). However, limited structure/function information on the Stt3 protein limits our understanding of how the poorly reactive amido group of the asparagine side chain is activated to form the N-glycosidic bond to the oligosaccharide (Igura et al., 2008, Maita et al., 2009). An OST identifies consensus acceptor sequences in polypeptides and modifies only some of the potential sites. Amino acids around the consensus sequence impact the probability that the
Le Paraquat, un Outil pour la Révélation Rapide d'Infections Fongiques Latentes et de Champignons Endophytes

Paraquat: a tool for the quick development of latent fungal infections and endophytic fungi. Detached winter wheat leaves without any symptom of fungal infection were thoroughly washed, surface desinfected, treated with paraquat (0.03–0.32% a.i.) and incubated on nutrient agar or in moist chambers under sterile conditions. Microscopic examinations showed that hypae and yeast cells emerged from several stomata within 48–72 h after treatment. Fungal colonies developed on agar within the same period of time. More than 27 filamentous fungal genera and yeasts were identified during a wheat cropin healthy, green leaves. Non-treated leaves showed very few early emergences of fungi from stomata, but senescent leaves eventually yielded several fungal taxa observed after paraquat treatment. Similar observations were made on non-detached wheat leaves, and on detached sugarbeet leaves. Paraquat also induced development of Fusarium spp. from detached healthy winter wheat ears before or after heading. In grape berries, paraquat induced the development of latent infections of Botrytis cinerea, a few days after treatment. The usefulness of paraquat for the detection of endophytes and for the diagnosis of early and latent fungal infections in plants, and the possible involvement of endophytes in tissue senescence are discussed.
How much grassland biomass is available in Ireland in excess of livestock requirements

Grassland is a dominant biomass resource in Ireland and underpins most animal production systems. However, other commercial uses for grassland biomass exist, inclu ding, for example, the production of biogas through anaerobic digestion for the generation of heat, electricity and transport fuel. The objective of this study was to estimate the annual grassland resource available in Ireland in excess of livestock requirements under six contrasting scenarios. Under current grassland management and production practices there is an estimated average annual grassland resource of ca. 1.7 million tonnes of dry matter (DM) available in excess of livestock requirements. Only a small proportion of this resource (0.39 million tonnes of DM per annum) would be available if the targets set out in ‘Food Harvest 2020’ were achieved. However, increasing nitrogen (N) fertiliser input (to the limit permitted by the E.U. Nitrates Directive) combined with increasing the grazed grass utilisation rate of cattle (from 0.60 to 0.80 kg DM ingested by livestock per kg DM grown) has the potential to significantly increase this average resource to 12.2 million t DM/annum, even when allowing for achievement of ‘Food Harvest 2020’ targets. Under these scenarios, alternative uses for grassland biomass such as anaerobic digestion and green biorefining would not compete with traditional dairy, beef and lamb production systems, but could provide an alternative enterprise and income to farmers.
Essential Oils as Green Pesticides : Potential and Constraints

Many plant essential oils show a broad spectrum of activity against pest insects and plant pathogenic fungi ranging from insecticidal, antifeedant, repellent, oviposition deterrent, growth regulatory and antivector activities. These oils also have a long tradition of use in the protection of stored products. Recent investigations indicate that some chemical constituents of these oils interfere with the octopaminergic nervous system in insects. As this target site is not shared with mammals, most essential oil chemicals are relatively non-toxic to mammals and fish in toxicological tests, and meet the criteria for “reduced risk” pesticides. Some of these oils and their constituent chemicals are widely used as flavoring agents in foods and beverages and are even exempt from pesticide registration. This special regulatory status combined with the wide availability of essential oils from the flavor and fragrance industries, has made it possible to fasttrack commercialization of essential oil-based pesticides. Though well received by consumers for use against home and garden pests, these “green pesticides” can also prove effective in agricultural situations, particularly for organic food production. Further, while resistance development continues to be an issue for many synthetic pesticides, it is likely that resistance will develop more slowly to essential-oil-based pesticides owing to the complex mixtures of constituents that characterize many of these oils. Ultimately, it is in developing countries which are rich in endemic plant biodiversity that these pesticides may ultimately have their greatest impact in future integrated pest management (IPM) programmes due to their safety to non-target organisms and the environment.
The Docking Protein FRS2α Is an Essential Component of Multiple Fibroblast Growth Factor Responses during Early Mouse Development

ABSTRACT The docking protein FRS2α is a major mediator of fibroblast growth factor (FGF) signaling. However, the physiological role of FRS2α in vivo remains unknown. In this report, we show that Frs2α-null mouse embryos have a defect in anterior-posterior (A-P) axis formation and are developmentally retarded, resulting in embryonic lethality by embryonic day 8. We demonstrate that FRS2α is essential for the maintenance of self-renewing trophoblast stem (TS) cells in response to FGF4 in the extraembryonic ectoderm (ExE) that gives rise to tissues of the placenta. By analyzing chimeric embryos, we found that FRS2α also plays a role in cell movement through the primitive streak during gastrulation. In addition, experiments are presented demonstrating that Bmp4 expression in TS cells is controlled by mitogen-activated protein kinase-dependent FGF4 stimulation. Moreover, both the expression of Bmp4 in ExE and activation of Smad1/5 in epiblasts are reduced in Frs2α-null embryos. These experiments underscore the critical role of FRS2α in mediating multiple processes during embryonic development and reveal a potential new link between FGF and Bmp4 signaling pathways in early embryogenesis.
Spawning and development of larvae and juveniles of the rare blue Mauritius angelfish, Centropyge debelius (1988), in the hatchery.

This study documents the rearing and life history stages of the rare blue Mauritius angelfish, Centropyge debelius, from spawning of eggs through sexual maturity. A C. debelius pair was maintained at our facility for 22 mo. The pair was conditioned to spawn for a 4-mo period in the fall of 2005 and a 4-mo period in the summer of 2006 using water temperature and photoperiod manipulation. Continuous spawning was achieved at water temperatures between 22 and 24 C and a photoperiod of long day (LD) 13.5:10.5. Over a 124-d period, the female produced 97 spawns, 59% of which resulted in fertile eggs. The average fecundity per spawn was 237 eggs (range 13‐813 eggs). Fertility of all preserved spawns averaged 19.0 ± 19.8%. Larval rearing attempts using wild caught zooplankton and Artemia nauplii resulted in a total of 10 C. debelius juveniles raised through metamorphosis with an average larval survival up through metamorphosis of 0.36%. Three resulting juveniles were raised through sexual maturity. Sexual dichromatism was first observed about 180 d posthatch. A statistical model: Y = (X × 0.32437) − (X 2 × 0.00043) − 2.004, where Y = total length (mm) and X = number of days in culture, explained 97.6% of the variation in growth ( P< 0.001, R 2 = 0.976). The development of eggs and larvae was observed to be similar to that of other Centropyge species that have been cultured. Results of this study indicate that the artificial propagation of C. debelius is technically feasible and forms the basis for this report.
A extração do manganês e suas formas de ocorrência em alguns solos do estado de São Paulo

O presente trabalho estuda a capacidade de extracao do manganes do solo, por diversas solucoes, a fim de esclarecer as formas de ocorrencia daquele elemento nos solos do Estado de Sao Paulo. Os solos estudados foram representados por tres amostras de terra roxa legitima (solo oriundo de diabase), tres amostras de solo massape-salmourao (solo proveniente de gnais, xistos, granitos, etc.) e duas amostras de solo arenito Bauru (solo derivado da rocha sedimentar denominada arenito Bauru). Para extrair o manganes foram usadas as solucoes : solucao normal de acetato de amonio com pH = 7,00 ; solucao normal e meio normal de nitrato de potassio ; solucao normal e meio normal de nitrato de sodio ; solucao normal de acetato de magnesio ; solucao normal de nitrato de calcio ; solucao normal de acetato de amonio, contendo 0,4% de hidroquinona e com pH = 7,00 ; solucoes de acido nitrico 0,01, 0,05 e 0,2 normal. As extracoes foram executadas por percolacao usando 100 a 200 ml das mesmas para 10 g de terra. Foi, tambem, executada uma extracao energica, usando-se H2SO4 (1+1) e HNO3 para conhecer o teor em manganes no estado de reserva. Os resultados obtidos mostraram que as solucoes dos sais de magnesio e calcio foram mais eficientes que as de acetato de amonio (sem hidroquinona), de nitrato de sodio e de nitrato de potassio, na extracao do manganes. As solucoes normais de nitrato de sodio e nitrato de potassio forneceram os resultados mais proximos dos obtidos com a solucao normal de acetato de amonio com pH = 7,00. A solucao de acetato de amonio contendo 0,4% de hidroquinona e com pH = 7,00 extraiu uma quantidade elevada de manganes, acontecendo o mesmo com as solucoes 0,01, 0,05 e 0,2 normal de acido nitrico. Os dados obtidos esclarecem que o manganes, alem da forma "trocavel", ocorre, nas amostras estudadas, na forma de oxidos hidratados, desde MnO.mH20 ate MnO2.nH2O e, provavelmente, em outras formas. Em virtude da relativa complexidade das formas de ocorrencia do manganes no solo, a extracao do teor "trocavel" exclusivo tornou-se dificil. Entretanto, admitindo-se como "trocavel" o teor extraido pela solucao normal de acetato de amonio com pH = 7,00, a solucao que mais satisfez, sob cs pontos de vista de capacidade de extracao e de facilidade de marcha analitica, foi a de nitrato de sodio normal. O teor de manganes extraido por qualquer das solucoes dos sais de amonio, sodio, potassio, calcio e magnesio das amostras estudadas, mostrou que a quantidade daquele elemento existente nos solos em questao e suficiente para satisfazer as exigencias da maioria das plantas cultivadas.
Field Observations on the Effect of a Mannan Oligosaccharide on Mortality and Intestinal Integrity of Sole (Solea senegalensis, Kaup) Infected by Photobacterium damselae subsp. piscicida

This study was conducted in order to investigate the effect of a mannan oligosaccharide (MOS) on the intestinal morphology of sole (Solea senegalensis, Kaup) reared under commercial conditions. The dietary inclusion rate for MOS was 0.4% and it was used either alone or in combination with a vaccination regime against bacterial diseases (Pasteurella spp. and Vibrio spp.). One week after the start of the experimental period, a natural outbreak of pasteurellosis, caused by Photobacterium damselae subsp.piscicida,occurred in all the groups of fish.A two-way ANOVA showed that only MOS supplementation reduced fish mortality by ca. 8% (P = 0.050). Additionally, light microscopy examination of the intestine revealed that MOS supplementation significantly increased the mucosal folding by 29% (P = 0.016) in the anterior intestinal region and by 33% (P = 0.002) in the posterior intestinalregion. Scanning electron microscopy demonstrated that both MOS supplementation and vaccination significantly increased microvilli density on the enterocyte surfaces in the anterior intestinal regionby 13% (P = 0.028) and 30% (P = 0.001) respectively. In the posterior intestinalregion neither MOS supplementation nor vaccination significantly affected the microvilli density (P = 0.005). The present study suggests that dietary MOS supplementation protects the intestinal morphology of infected sole and hinders the development of pathogenic infection, possibly by binding with Photobacterium damselae subsp. piscicida, resulting in reduced mortality of infected fish.
A cytogenetic study on the Angora breed of goat (Capra hircus) reared in Turkiye.

irkla ilgili kapsamli bir sitogenetik calismaya rastlanmamistir. Sunulan on sitogenetik calisma irkin temel kromozomal yapisini arastirmak ve populasyon duzeyinde sitogenetik calismalara baslangic yapmayi amaclamaktadir. Kan kulturleri hem geleneksel metoda gore ve hem de Timidin metoduna gore duzenlenmistir. Geleneksel ve GTG-RBA-RBG band karyotipleri elde edilerek irkin kromozomlarinin sentromer indeksleri belirlenmistir. Band modeli karsilastirmalari Ankara keci irkinin keci turu icin standardize edilmis RBA-RBG band modeli ile benzerligini dogrulamistir. Bu calisma sonucunda Ankara kecisi irkinda populasyon duzeyinde sayisal ve yapisal kromozom anomalilerinin tasiyicilarinin tanimlanmasi, irkin verim ozeliklerinin gelistirilmesinde daha ileri duzeyde sitogenetik calismalara ihtiyac duyuldugu degerlendirilmistir
Effects of exogenous nitric oxide on photosynthesis, antioxidative ability, and mineral element contents of perennial ryegrass under copper stress

A hydroponics experiment was conducted to test the effects of sodium nitroprusside (SNP, a donor of NO) supplied with different concentrations on copper (Cu) toxicity in ryegrass seedlings (Lolium perenne L.). Excess Cu (200 µM) reduced chlorophyll content, resulting a decrease in photosynthesis. Cu stress induced the production of hydrogen peroxide (H2O2) and superoxide anion (O2• −), leading to malondialdehyde (MDA) accumulation. Furthermore, activities of antioxidant enzymes in Cu-treated seedlings such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were decreased. In addition, Cu stress inhibited the uptake of K, Mg, Fe, and Zn and increased Ca content in roots. Moreover, in leaves of Cu-stressed seedlings, K, Fe, and Zn contents were decreased and the contents of Ca and Mg were not affected significantly. In Cu-treated seedlings, Cu concentration in roots was higher than in leaves. Addition of 50, 100, 200 µM SNP in Cu-mediated solutions increased chlorophyll content and photosynthesis, improved antioxidant enzyme activities, reduced Cu-induced oxidative damages, kept intracellular ion equilibrium under Cu stress, increased Cu concentration in roots and inhibited Cu accumulation in leaves. In particular, addition of 100 µM SNP had the best effect on promoting growth of ryegrass seedlings under Cu stress. However, the application of 400 µM SNP had no obvious alleviating effect on Cu toxicity in ryegrass seedlings.