Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in fungal endophyte communities of pedunculate oak (Quercus robus L.)

Fungal endophytes are a taxonomically and ecologically heterogeneous group of ubiquitous intercellular fungi that live part of their life within the tissues of the plants without causing apparent harm to the host. They may contribute to the stress tolerance and resistance of the plants, and endophytes may also be involved in decomposition processes. Thus, these fungi are an interesting part of biodiversity e.g. in forest ecosystems. Little is still known about the temporal and spatial patterns in endophyte community structures in trees. Moreover, while it is known that endophytes spread to trees from the environment (horizontally) it is not clear at which scales their spreading occurs, and if e.g. neighbouring vegetation determines endophyte communities in trees. In addition, it is not known if the general vitality of the trees affects the frequency and diversity of endophyte infections in trees. Using culture-dependent method (isolations), endophyte communities were compared in young pedunculate oak (Quercus robur L.) trees that were surrounded by herbs and shrubs in different combinations and that showed different vitality status. The isolations were done from current and previous year’s twigs (xylem and bark) in early and late summer to study the temporal and within-tree spatial patterns. A total of 384 samples were plated with bark and xylem pieces. Altogether 172 of them produced a total number of 285 isolates, which could be grouped in 22 morphological groups (morphotypes). The colonisation and isolation rate values showed the succession of endophyte communities during the season and inside the twigs but there were no significant effects of tree vitality on these rates. However, in June the declining trees had higher morphotype evenness, indicating that declining trees were compromised in their ability to defend themselves against fungal infections, which may have reduced the competition between the different invading fungi. The Jaccard’s similarity index and Shannon’s diversity index showed that there was no clear pattern of infection from the closest surrounding vegetation, suggesting that the spreading of these fungi occurs at a larger scale.
Ecological genetics and conservation genomics of wolf (Canis lupus)

In the present work, we apply both traditional and Next Generation Sequencing (NGS) tools to investigate some of the most important adaptive traits of wolves (Canis lupus). In the first part, we analyze the variability of three Major Histocompatibility Complex (MHC) class II genes in the Italian wolf population, also studying their possible role in mating choice and their influence on fitness traits. In the second section, as part of a larger canid genome project, we will exploit NGS data to investigate the transcript-level differences between the wolf and the dog genome that can be correlated to domestication.
Effect of organic manures on productivity, soil fertility and economics of soybean (Glycine max) - durum wheat (Titicum durum) cropping system under organic farming in Vertisols

A field experiment was conducted during 2003-06 on deep Vertisols of Bhopal to study the effect of 3 organic manures, viz poultry manure, vermicompost and cattledung manure vis-a vis chemical fertilizers on the productivity, soil fertility and economics of soybean (Glycine max L. Merr.) - durum wheat (Triricum durum Desf.) cropping system. In the first year (2003-04), chemical fertilizers recorded significantly higher yield of crops and application of organic manures recorded 7.3 to 13.3 % reduction in soybean yield and 7.8 to 14.8 % reduction in wheat yield. In the second year (2004-05), soybean yield was on par among the nutrient sources and wheat yield was on par between chemical fertilizers and poultry manure treatment. In the third year (2005-06), application of organic manures recorded similar yields to that of chemical fertilizers and in fact, poultry manure application resulted in 17.5 and 3.2 % higher yields of soybean and wheat, respectively, over the chemical fertilizers. The protein and oil content of soybean was not affected among the treatments but the protein content of wheat was lower in control compared to the application of either chemical or organic manures. At the end of the 3 cropping cycles, soil organic carbon, available N, P, K status and enzyme activity of soil (dehydrogenase and phosphatase activity) were significantly improved in organic manure treatments compared to chemical fertilizers. The economics of soybean - durum wheat cropping system was in favour of chemical fertilizers during the first 2 years but in the third year, organic farming resulted in better economic returns due to improved productivity and lower cost of cultivation compared to chemical farming.
Screening of chilli germplasm against yellow mite and its management

Among the 36 germplasm chilli lines (Capsicum annuum L.) were screened against yellow mite (Polyphagotarsonemus latus) during 2003, none was found immune. However, genotype HC28 × LCA was least susceptible against this pest. The efficacy study conducted during 2004 and 2005 suggested that insecticide Prempt 20EC (a ready-mix of fenpropethrin 15%+ pyriproxifen 5%) @750 ml/ha was most effective in reducing mite population. With about 62.7% reduction in mite population, this mixture maintained its persistence up to 10 days after application. This best treatment (Prempt 20 EC) was further tested during 2006 at farmer fields in two locations along with earlier recommended insecticides viz., endosulfan (Thiodan 35 EC) and methyldemeton (Metacystox 25 EC) @750 ml and 650 ml/ha, respectively. Highest cost: benefit ratio of 1:5.7 recorded for Prempt 20EC was followed by 1: 2.4 of Thiodan 35EC and 1: 1.19 of Metacystox 25EC. These findings have potential recommendation for adoption by farmers for the control of yellow mite in chilli crop.
Towards a molecular and functional characterisation of sensory-neurosecretory cells in Platynereis dumerilii and fish

Das Gehirn wird oft als integratives Organ beschrieben, welches Informationen von peripheren sensorischen Organen bekommt, prozessiert und einen bestimmten Output erzeugt. Jedoch kann das Gehirn nicht nur Informationen prozessieren, es ist auch in der Lage selbst Informationen aufzunehmen. Es wurden im Gehirn von einigen Spezies Zellen beschrieben, die direkt sensorisch sind. Diese Zellen sekretieren oft auch neuronale Hormone und bilden den anzestralen Kern des Wirbeltiergehirns. Wir arbeiten an einem bestimmten Typ dieser sensorischen neurosekretorischen Zellen. Diese exprimieren ein wahrscheinlich licht-sensitives Opsin Protein und sekretieren ein neuronales Hormon der Nonapeptid Superfamilie, namlich Vasotocin. Diese Zellen sind hochst konserviert und wurden in Fischen sowie in Wurmern entdeckt. Daher mussen diese Zellen im gemeinsamen Vorlaufer der beiden Spezies bereits existiert haben (Urbilateria) (Tessmar-Raible, 2007). Unsere Hypothese ist, dass dieser Zelltyp ein anzestrales, hochkonserviertes Minimalmodul reprasentiert, das die Sekretion von Vasotocin reguliert. Das beruht auf der Beobachtung dass in einigen Spezies die Sekretion von Vasotocin mit den spezifischen Reproduktionszyklen korreliert. Diese Reproduktionszyklen werden meist uber exogene Lichtzyklen reguliert. Das Ziel meiner Diplomarbeit war es verschiedene Aspekte dieses Systems genauer zu untersuchen, um schlussendlich zur funktionellen Charakterisierung von diesem sensorisch-neurosekretorischem Zelltyp beizutragen. Ich arbeitete an drei verschiedenen Projekten. Das erste Projekt umfasst die Charakterisierung einiger Aspekte des Nonapeptid Hormonsystems in Platynereis dumerilii. Im Rahmen des zweiten Projektes habe ich untersucht wie die Expression von vasotocin in Vertebraten reguliert wird. Abschliesend habe ich neue wahrscheinlich licht-sensitive Mitglieder einer Photorezeptorfamilie in Vertebraten identifiziert und charakterisiert.
Enhanced antitumor effect of axitinib synergistic interaction with AG490 via VEGFR2/JAK2/STAT3 signaling mediated epithelial-mesenchymal transition in cervical cancer in vitro

Abstract Background: Epithelial to mesenchymal transition (EMT) not only confers tumor cells with a distinct advantage for metastatic dissemination, but also it provides tumor cells for proliferation and chemotherapy resistance. Thus, inhibiting this process using single or multiple agents, remains a field of intensive research. The development of EMT has been implicated in not only conferring cancer cells distant metastasis, but also providing tumor cells advantages for proliferation and chemotherapy resistance. Objective: We investigated whether axitinib synergistic interaction with AG490 could effectively block the growth and EMT-mediated tumor metastasis in cervical cancer in vitro. Methods: We addressed synergism effects on tumor growth, axitinib, AG490 alone and in any possible combinations on cell viability, apoptosis and cell cycle distribution were evaluated by XTT assay, Annexin V/propidium iodide staining and flow cytometric analysis. To assess how combination therapy affected chemotactic motility in tumor cells, wound-healing migration and the Boyden chamber invasion assays were applied in vitro. Further, using western blots, the key signaling molecules and pathways in response to axitinib and AG490 combination treatment in anti tumor growth and anti EMT-mediated tumor metastasis were analyzed in Hela cells. Results: Therapy with axitinib and AG490 resulted in strong synergistic inhibition of proliferation, migration and cell cycle arrest without potently effect on apoptosis induction relative to AG490 monotherapy and control in vitro. Furthermore, phosphorylation of VEGFR2 (Tyr1175), JAK2 (Tyr1007/1008) and STAT3 (Tyr705) was completely blocked in parallel with significant reduction expressions of N-cadherin and obvious enhancement levels of E-cadherin through down-regulating Snail responding to combination treatment in cervical cancer cells. Conclusion:We first provided evidences that combination therapy of axitinib and AG490 significantly enhances anti-tumor effect via VEGFR2/JAK2/STAT3 signaling mediated growth arrest and EMT-mediated tumor metastasis inhibition, holds promise for an efficacious treatment of these advanced patients.
Survival rates and breeding biology of Puffins on Skomer Island, Wales

Puffins Fratercula arctica were studied on Skomer Island, Wales (51? 44'N, 5019'W) during 1972-77. Annual survival of breeding adults was 95%. Each year, 20-27% adults were without nesting burrows, and 2% were absent from the colony. 64% of pairs with burrows fledged a chick, with 5-16% not laying, 22-25% eggs not hatching, and 5% chick mortality. Much of the egg loss was caused by disturbance from prospecting Manx Shearwaters Puffinus puffinus which competed with Puffins for burrows. Data on the feeding and growth of chicks is given. Young Puffina first returned to the colony at two, or more usually three, years old. Four years was the earliest age for first breeding. At least 10-16% fledglings survived to four years old; it was not clear whether enough survived to replace adult mortality.
Shell Egg Sanitation: UV Radiation and Egg Rotation to Effectively Reduce Populations of Aerobes, Yeasts, and Molds.

The intensity of UV radiation (254 nm) and egg rotation were examined for their effect on aerobic microorganisms, yeast, and mold on egg shell surfaces. Aerobic microorganisms, yeast, and mold populations were significantly reduced by UV treatments at 1,720 μW/cm2. Eggs rotated at 1 revolution per min under 1,720 μW/cm2 of UV light had significantly reduced populations of aerobic microorganisms. Higher intensity (4,350 μW/cm2) with egg rotation also significantly decreased aerobic microorganism populations. Eggs treated with rotation and 15 min of 4,350 μW/cm2 of UV radiation had significantly lower populations of aerobic microorganisms than eggs without rotation. Eggs rotated and exposed to 15 min of 4,350 μW/cm2 of UV were compared to eggs dipped in 200 ppm chlorine-treated water solution for 1 min, exposed to 3 × formaldehyde fumigation for 20 min, sprayed with commercial sanitizer (Bioguard®) for 3 min, and eggs receiving no treatment. Eggs treated with UV radiation had significantly higher populations of aerobic microorganisms than eggs from other treatments but significantly lower bacterial populations than the control group. Mold and yeast populations of UV-treated eggs were significantly lower than the untreated eggs. The results of this study indicate that UV radiation can significantly reduce aerobic microorganisms, yeast and molds on egg shell surfaces.
Mechanisms underlying thymidylate synthase regulation in human cells

Thymidylate synthase (TS) catalyzes the last step of the only de novo synthesis pathway for deoxythymidine monophosphate (dTMP), a nucleotide required for DNA synthesis and repair. The central role of TS in nucleic acid metabolism has made it an attractive target for antineoplastic drugs. 5-fluorouracil is a prototypic drug targeting TS activity, which blocks the enzyme by forming a stable inhibitory complex with the protein. Depletion of dTMP following TS inhibition leads to repeated cycles of incorporation of uridine into DNA, causing single strand breaks, and ultimately triggering apoptosis. TS is commonly believed to be a S-phase dependent enzyme, an assumption largely based on a score of studies performed in rodent cells. Recent reports do not support this view and suggest that TS is a cell proliferation marker rather than a S-phase enzyme. The mechanisms controlling TS expression in human cells are poorly understood and could potentially provide new therapeutics approaches to decrease TS levels in cancer cells and to sensitize them to anti-TS drugs. We showed that, in human cells synchronized by serum starvation or subjected to serum deprivation, the expression patterns of TS and cyclin E (a well characterized E2F target) were significantly different. Ectopic expression of E2F1 or cyclin E had no effect on TS levels. However, inhibition of CDK4 but not CDK2 was associated with a clear decrease in TS levels in human cells. We also demonstrated that inhibition of MEK1 was associated with a decrease in TS levels, but this event was independent of ERK2 activity. Using reporter assays, we showed that MEK1 controlled TS promoter transcription, and that deletion of the Sp1 site from the essential promoter region greatly reduced the ability of MEK1 to stimulate the TS promoter. Surprisingly, unlike in rodent cells, LSF and GABP failed to
The role of mtDNA damage in mitochondrial dysfunction

Mammalian mitochondria have a 16.5 kb genome encoding for 13 polypeptides, 2 rRNAs, and 22 tRNAs essential for mitochondrial function. Mutations and deletions in mitochondrial DNA (mtDNA) are implicated in some hereditary diseases as well as aging, cancer and neurodegeneration. Here, we examine the role of DNA ligase in mtDNA maintenance, and the role of mtDNA damage inflicted by hydrogen peroxide (H2O2) or methyl methanesulfonate (MMS) in mitochondrial dysfunction. We establish that mitochondrial DNA ligase activity is essential for survival, persistent mtDNA damage is not sufficient to induce rapid mtDNA loss and mitochondrial dysfunction. We removed and replaced the normal mitochondrial DNA ligase III with different forms of mitochondrially-targeted DNA ligase, and found that mitochondrial DNA ligase activity is necessary for cellular survival and that any type of DNA ligase activity in the mitochondria is sufficient to maintain mtDNA integrity and copy number. To study the relationship between mtDNA integrity and mitochondrial function, we treated cells with H2O2 or with the alkylating agent MMS, both of which resulted in persistent mtDNA lesions. However, only the H2O2-treated cells showed mtDNA loss and mitochondrial dysfunction by 8 hours post-treatment, indicating that persistent mtDNA damage does not necessarily cause a rapid loss of mtDNA or mitochondrial function. These data suggest that oxidants are more efficient than alkylating agents at driving mtDNA loss and mitochondrial dysfunction. We then addressed the cause of H2O2-induced loss of mtDNA 8 hours following treatment. We hypothesized that this loss of mtDNA is dependent upon mitochondrial fission and mitophagy. In order to test this hypothesis, we treated cells with the fission inhibitor mdivi-1. Mdivi-1 protected mtDNA against oxidative-induced mtDNA damage but not MMS-induced mtDNA damage. Because mdivi-1 is thought to act through inhibition of Drp1, we performed siRNA-mediated knockdown (KD) of Drp1 and observed that the knockdown did not recapitulate mdivi-1 treatment in protecting against H2O2-induced mtDNA damage. Furthermore, treating Drp1 KD cells with mdivi-1 still showed the protective effects of mdivi-1 on mtDNA damage. These results suggest that the mdivi-1 mediated protection of oxidant-induced mtDNA damage may be independent of its role in inhibiting mitochondrial fission.
Human dimensions of invasive alien species.

The American grey squirrel, introduced to Italy and the British Isles as a pet species, replaces the native red squirrel through competitive exclusion. The potential expansion of the Italian population to the Alps and to a large portion of Eurasia represents a major threat to biodiversity at a continental scale. An eradication project of the Italian population, supported by most non-government organisations, failed because of the strong opposition by radical animal rights groups. In mainland eradications, time is constrained and delays caused by opposition can determine the failure of the entire campaign. Information may be irrelevant for reducing conflicts, because primary differences exist between animal rights and conservation groups. In these cases, a political decision needs to be taken. Awareness raising, revision of the legal framework, consultation processes, and the creation of biosecurity agencies, appear fundamental steps for effectively addressing the threats posed by invasive alien species.
Lenticel discolouration in mango (Mangifera indica L.) fruit – a cytological study of mesophyll cells from affected tissue

Summary Mango fruit is characterised by the presence of lenticels, with some cultivars prone to a condition known as ‘lenticel damage’. The condition manifests itself as a localised red-to-dark discolouration around the lenticels. The presence of these unacceptable spots on mature green fruit has economic implications. The cytological nature of lenticel discolouration was investigated as part of a study of affected mango fruit. Lenticels were dissected from physiologically mature fruit in predetermined groups of varying discolouration. Transmission electron microscopy and light microscopy of mesophyll cells from affected tissue indicated conservation of cellular structures and endomembranes in all variants of discolouration. It was therefore shown that the accumulation of cell wall-bound phenolics does not result from structural damage such as vacuolar collapse or membrane disintegration. Results further suggest the apoplastic transport of the signal for phenolics deposition. Accumulation of phenolic compounds in a distinct zone of affected tissue around the lenticel creates a barrier between the atmosphere and the rest of the mesophyll. Although lenticel discolouration is an inherent self-defence mechanism supported by continued metabolic activity, it is a superficial, cosmetic defect.
Leaf litter bags as an index to populations of northern two-lined salamanders (Eurycea bislineata)

Concern about recent amphibian declines has led to research on amphibian populations, but few statistically tested, standardized methods of counting amphibians exist. We tested whether counts of northern two-lined salamander larvae (Eurycea bislineata) sheltered in leaf litter bags-a relatively new, easily replicable survey technique-had a linear correlation to total number of larvae. Using experimental enclosures placed in streams, we compared number of salamanders found in artificial habitat (leaf litter bags) with total number of salamanders in each enclosure. Low numbers of the animals were found in leaf litter bags, and the relative amount of variation in the index (number of animals in leaf litter bags compared to total number of animals in stream enclosures) was high. The index of salamanders in leaf litter bags was not significantly related to total number of salamanders in enclosures for two-thirds of the replicates or with pooled replicates (P= 0.066). Consequently, we cannot recommend using leaf litter bags to index populations of northern two-lined salamanders.
Ovulation rate and litter size of prolific Inverdale (FecX I) and Hanna (FecX H) sheep.

Two mutations, Inverdale (FecX) and Hanna (FecX), that affect ovulation rate in sheep have been identified at the FecX locus. Ewes with two copies of the FecX or FecX alleles are known to be infertile, but heterozygous ewes have increased ovulation rate and litter size. Ovulation rate and litter size were compared between heterozygous Inverdale ewes (I+) and heterozygous Hanna ewes (H+). The effect of the FecX and FecX alleles on ovulation rate in heterozygous ewes was an increase of 0.80-1.32 compared to non-carriers, and there was no significant difference between the two alleles. Litter size increased by 0.35-0.81, with no significant difference between the two alleles. Consequently, the same breeding strategies can be applied to sheep carrying either allele.
The life cycle of Tityus (Atreus) neblina Lourenço, 2008 (Scorpiones, Buthidae) in Cerro de la Neblina,: Brazil/Venezuela.

Biological observations were made on specimens of Tityus (Atreus) neblina Lourenco, 2008 collected the region of 'Cerro de la Neblina', on the border between Brazil and Venezuela. The total duration of embryonic development ranged be- tween 4.7 and 21 months. It is suggested, however, that durations exceeding 6 months undoubtedly correspond with seasonal diapause. The moults necessary to reach the various juvenile instars and adulthood took place at average ages of: 4, 83, 239, 413 and 606 days. These developmental periods are significantly longer from those in other medium-sized species of Tityus, but are similar to those previously observed among large species of the genus. Morphometric growth values of the different in- stars are similar to those in other known species of Tityus. A new example of parthenogenesis is confirmed in Tityus neblina.