Miracle-dz/UniFAR-FTUs huggingface dataset:
Spawning and early development of the West Indian top shell, Cittarium pica (Linnaeus, 1758), under ex-situ conditions

The West Indian top shell, Cittarium pica , is an endangered vetigastropod from the rocky intertidal Caribbean. In order to provide a basis for its hatchery-production as a conservation tool, spawning and early development were evaluated under ex-situ conditions. Spawning response was monitored during different lunar phases with application of physical and chemical stimuli – such as changes in temperature salinity and desiccation, exposure to UV irradiated water and chemical stimulation with Tris and hydrogen peroxide. Spawning response was obtained in association with daytime, new moon, flooding and high tides. Use of physical and chemical stimuli did not elicit any spawning response. Adults conditioned in the hatchery for one year did not spawn. Spawning of males and females was simultaneous and frequently intermittent. On average, percentage and size of spawn was higher for males than females. Fecundity was positively correlated with total female wet weight, with an average value of 149 000 oocytes per female. Embryonic and larval development was reported in detail. Results suggest that there is a high potential to use the controlled ex-situ reproduction of C. pica as a conservation tool, since gamete and larvae were repeatedly obtained from wild adults collected days before new moon following a circadian endogenous pattern applying simple protocols of spawning, fertilization and incubation.
Is there a relation between Murine double minute 2 T309G polymorphism and lung cancer risk in the Turkish population?

Abstract Introduction Association between Murine double minute 2 T309G polymorphism and lung cancer risk has been investigated in several populations, but results of these studies are inconsistent. We aimed to investigate the effect of Murine double minute 2 T309G polymorphism on development of lung cancer in a Turkish population. Methods Total 200 subjects including 100 patients and 100 controls were analyzed and used polymerase chain reaction and restriction fragment length polymorphism methods for genotyping analysis of the polymorphism. Results We found that smokers compared with non-smokers have approximately eight fold higher lung cancer risk [p=0.0001, OR=8.27 (4.02–16.9)]. Frequency of GG genotype was higher in patients than in controls, but this ratio was not significant (χ2=3.5, p=0.17). Genotype distribution of the polymorphism was not different neither patients with non-small cell lung cancer nor patients with small cell lung cancer (χ2=2.89, p=0.57). We analyzed together with demographic feature (except smoking habit), clinicopathological findings and genotype frequencies of this polymorphism, and any association with lung cancer risk was not obtained. Conclusion No correlation between Murine double minute 2 T309G polymorphism and lung cancer risk was detected in this Turkish population.
Indirect genetic effects for group-housed animals

ABSTRACT Alemu, SW(2015) Indirect Genetic effects for Group-housed Animals. Joint PhD thesis between Aarhus University, Denmark and Wageningen University, the Netherlands. Social interactions among individuals are common both in plants and animals. With social interactions, the trait value of an individual may be influenced by the genes of its interacting partners, a phenomenon known as indirect genetic effects (IGE). An IGE is heritable effect of an individual on trait values of another individual. A large body of literature has shown that social interactions can create addition heritable variation in both plants and animals, for both behavioural and production traits. When IGE are estimated it is usually assumed that an individual interacts equally with all its group mates, irrespective of genetic relatedness. This assumption may not be true in mixed groups of kin and non-kin, where an individual may interact systematically different with kin and non-kin. Current IGE models ignore such systematically different interactions between kin and non-kin. Thus, the main aim of this thesis was to develop and apply statistical methods to estimate IGE when interactions differ between kin and non-kin. Social interactions are important in mink that are kept in groups for the production of fur. Group housing of mink increases aggression behaviours, which is reflected by an increase in the number of bite marks on the pelts, and reduces the welfare of the animals. We estimated the genetic parameter for bite mark traits in group-housed mink, to investigate the prospects for genetic improvement of bite mark traits. We found that there are good prospects to produce mink that have a low level of biting. Finally, we further concluded that genetic parameter estimation for bite mark score should take into account systematic interactions due to sex or kin. In this thesis we also investigated genomic selection for socially affected traits, considering survival time in two lines of brown egg layers showing cannibalistic behaviour. Despite the limited reference population of ~234 progeny tested sires, the accuracy of estimated breeding values (EBV) was ~35% higher for genomic selection compared with the parent average-EBV. We found that the response to genomic selection per year for line B1 was substantially higher than for the traditional breeding scheme, whereas for line BD response was slightly higher than for the traditional breeding scheme. In conclusion, genetic selection with IGE combined with marker information can substantially reduce detrimental social behaviours such as cannibalism in layers and biting in group-housed mink.
Varieties of English and Kachru’s Expanding Circle

In this overview article, we present the motivations for compiling this issue of RJL and summarize the major premises of the World Englishes (WE) Paradigm. The focus is on the relations between the WE school of thought and the paradigms that branched from it, i.e. English as a Lingua Franca (ELF) and English as an International Language (EIL). The statuses of Englishes in the Kachruvian Expanding Circle that function mainly as lingua francas in international communication is one of the most controversial issues in sociolinguistics. We discuss the misconceptions regarding the Expanding Circle Englishes. Finally, we give a brief survey of the articles contributed to this issue, which develop theoretical and empirical material for the WE paradigm.
Methane and carbon dioxide emissions from lactating dairy cows grazing mature ryegrass/white clover or a diverse pasture comprising ryegrass, legumes and herbs

There is a growing interest in forage mixtures (Diverse pasture; e.g. containing grasses, legumes and herbs), especially those with a greater tolerance of dry conditions and a decreased nitrogen (N) content (reducing N losses), compared with ryegrass (Lolium perenne L and Lolium multiflorum L)/white clover (Trifolium repens L) pastures (RyeWC), which dominate New Zealand pastoral systems for dairy production. However, the effect of alternative forages on enteric methane (CH4) emissions is not known. The objective of the present trial was to compare CH4 emissions and milk production from dairy cows grazing either mature RyeWC or mature Diverse pasture (both approximately with pasture mass of 5600 kg DM/ha). The Diverse mixture comprised ryegrass, white clover, lucerne (Medicago sativa L), chicory (Cichorium intybus L) and plantain (Plantago lanceolata L). Milk production, measured from cows commencing at ~162 days of lactation, was less when cows grazed RyeWC than Diverse pastures (15.4 vs 16.7 kg/day; P < 0.001), whereas CH4 production (g/day) was similar for the respective treatments (411 g/day; P = 0.16). Milk composition was not affected by diet and CH4 intensity was similar for both diets (22 g/kg fat- and protein-corrected milk; P = 0.31). Methane yield [g/kg predicted dry matter intake (DMI)] averaged 22.6 and 24.9 for cows grazing RyeWC and Diverse pastures, respectively (P = 0.006). In conclusion, although the CH4 yield was greater when Diverse pasture was grazed, relative to RyeWC, there were no differences in emissions intensity or total CH4 emissions.
Ethanolic Allium sativum extract down-regulates the pelF gene involved in Pseudomonas aeruginosa biofilm formation

Exploration of efficacious plant extracts that can reduce or inhibit Pseudomonas aeruginosa biofilm formation is necessary. Allium sativum is a suitable candidate because of its relative abundance. This study was carried out to determine the effect of ethanolic A. sativum extract on the expression of the P. aeruginosa biofilm gene, pelF. The presence of the pelF gene in the isolates used for this study was confirmed via polymerase chain reaction (PCR) and agarose gel electrophoresis. P. aeruginosa cultures treated with 1 g/ml of the A. sativum extract had the least turbidity (6.7 absorbance value at A600). The expression profile of the pelF gene in the treated cultures was determined via PCR using cDNA synthesized from RNA isolated from the treated P. aeruginosa cultures. The amplicons from the PCR were analyzed via agarose gel electrophoresis and a concentration dependent down-regulation of the pelF gene was observed. Further quantification of the pelF gene’s expression was performed via real-time PCR using rpoB as the reference gene. A 4-fold down-regulation of the gene was observed at 0.5 and 1 g/ml concentrations, respectively. This study suggests that the suppression of the pelF gene of P. aeruginosa by A. sativum extracts plays a role in the inhibition of P. aeruginosa biofilm formation. This is the first study to elucidate the effect of A. sativum on the expression of any of the pel genes. Key words: Allium sativum, biofilm, cDNA, down-regulation, gene expression, pelF, Pseudomonas aeruginosa, quantitative polymerase chain reaction (qPCR).
Rapamycin, Inhibitor of Mtor Kinase, Sensitizes Leukemia Cells to Fludarabine-Induced Apoptosis, but Protects Survival of Normal Lymphocytes.

Background: The mTOR kinase inhibitor, rapamycin (RAPA), inhibits cell growth by G 1 phase cell cycle arrest. RAPA-induced cytotoxicity against acute lymphoblastic leukemia (ALL) cells was recently reported. Aim: We investigated cytotoxicity of RAPA alone or in combination with fludarabine (FA), a cytostatic active in G 1 phase, in ALL cells as well as in healthy lymphocytes. Methods: NALM-6 cells (pre-B ALL-derived cell line), and phytohemaglutynin (PHA)-stimulated normal lymphocytes were treated for 24–48h with different concentrations of RAPA (0,05–500ng/ml), alone or in combination with 0.1–50.0mM FA. Some samples were initially incubated with RAPA for 24h and then FA was added for the next 24h. Untreated cultures and treated with RAPA, FA or PHA alone served as respective controls. The pro-apoptotic effect was assessed by both Annexin-V and TUNEL assays and presented as an apoptotic index (AI). Cell cycle was analyzed by DNA content distribution in propydium iodide/RN-ase stained cells. Additionally, intracellular expression of cyclin A, D3 and E was evaluated. All fluorescence measurements were performed by flow cytometry. Overall cytotoxicity was evaluated by MTT assay. Results: RAPA was found to exert dual effect on NALM-6 cells. In lower concentrations (0.05–5ng/ml) RAPA exclusively inhibited proliferation, arresting NALM-6 cells in G 1 phase of cell cycle. An increasing evidence of apoptosis, along to enhancing cytotoxicity in MTT assay was observed higher RAPA doses (10–500ng/ml). When NALM-6 were treated with RAPA+FA, the highest AIs were found for the combination of 0.5 or 1.0ng/ml RAPA with 1nM FA. Median AI induced at 24h by 1.0ng/ml RAPA+FA was 12.4%, comparing to with RAPA or FA alone (AIs 1.9% and 4.8%, respectively; both p Conclusions: In low concentration RAPA sensitizes NALM-6 cells to FA-induced apoptosis. Pretreatment with RAPA enhances cytotoxic effect on leukemia cells, but not on normal lymphocytes. RAPA administrated prior to FA blocks reversible cell cycle progression, preventing lymphocyte from FA cytotoxicity. These data provide rationale for future applying RAPA in the combination with purine nucleoside analogues for treatment of lymphoproliferative diseases. Moreover, they suggest, that the choice of optimal doses of both RAPA and the cytostatic may result in selective anti-tumor treatment, with protection of normal cells.
Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay?

Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life’s origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life’s origins between mica sheets: (1) that potassium is essential for life’s origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life’s origins.
House sparrows offset the physiological trade-off between immune response and feather growth by adjusting foraging behavior

Growing feathers and mounting immune responses are both energetically costly for birds. According to the life history trade-off hypothesis, it has been posited that the costs of feather growth lead to temporal isolation between molt and other expensive activities, reproduction for example. In contrast to life cycle events, the need to mount an immune response can occur at any time, including during feather growth. Thus, we hypothesized that mounting an immune response during feather growth may divert energy and resources from feather growth and impair feather renewal. To test this hypothesis, we clipped or plucked the same feathers of male house sparrows, Passer domesticus biblicus. In the clipped group (n = 16), the feathers were absent with no regrowth; in the plucked group (n = 14), feathers were absent and regrowth was initiated. We also had an intact control group of 15 sparrows. We then initiated an inflammatory immune response by subcutaneous injection over the left breast muscle of the birds with a lipopolysaccharide (LPS) and quantified behavioral and physiological responses. We predicted that sparrows with plucked feathers would incur the highest energetic costs while mounting an immune response, and would increase their foraging effort to offset this cost. We found no difference in body mass and resting metabolic rates among sparrows subjected to the different feather and immune treatments. However, we did find that while sparrows with plucked feathers increased foraging efficiency following the immune challenge by paying fewer but longer visits to the food tray, allowing them to maintain food consumption. Foraging efficiency in sparrows with clipped feathers was reduced. We also found that quality of newly grown feathers after the immune challenge was poorer in the plucked group, suggesting that mounting an immune response competes with feather growth for resources. This article is protected by copyright. All rights reserved.
17β-Estradiol as a Neuroprotective Agent

The pathophysiology of neurodegeneration in the central nervous system is complex and multifactorial in nature and yet to be fully understood. Broad-spectrum neuroprotective agents with multiple mechanisms of action rather than a single druggable target are, therefore, highly desirable. The main human estrogen, 17β-estradiol, can also be considered a neurosteroid as it forms de novo in the central nervous system, and it possesses beneficial effects against practically all critical contributors to neu rodegeneration to collectively thwart both the initiation and the progression of neu- ronal cell death. This chapter details the main aspects of the hormone’s genomic and non-genomic actions important to protect the highly vulnerably neurons of the central nervous system, as well as translational efforts to successfully realize its powerful neu roprotective potential in clinical setting while ensuring both therapeutic safety and efficacy.
Flightless rails (Aves: Rallidae) from the early Miocene St Bathans Fauna, Otago, New Zealand

While known for over a decade to exist, fossil rails of the early Miocene (19–16 Ma) St Bathans Fauna, from the South Island of New Zealand, have not previously been described taxonomically or studied in detail. Here we use qualitative osteological features and analyse measurements from wing and leg bones to determine the number of taxa represented, their flight ability, and the presence and nature of sexual dimorphism within the identified taxa. We describe two new rail species in monospecific genera from the St Bathans Fauna: Priscaweka parvales gen. et sp. nov., which is extremely common, and Litorallus livezeyi gen. et sp. nov., a distinctly larger, uncommon species. Priscaweka parvales exhibited a significant degree of sexual dimorphism and was tiny, being the size of the extinct Chatham Island Rail Cabalus modestus. Both newly described species exhibit skeletal proportions and osteological features that indicate they had reduced wings and were flightless. These observations reveal that flightless rallid species have been present in New Zealand for millions of years. The distinctiveness of the St Bathans rails from their closest geographical and chronological neighbours suggests some hidden diversity of volant rails in Australia's fossil record. However, the combined data from Australasian and European records reveal no evidence for a diverse early Miocene crown rallid fauna as predicted by some molecular studies. A subsequent, middle Miocene radiation for crown rallids seems more likely, and appears to have produced the high taxonomic diversity seen in Holocene Australasian rail faunas. http://zoobank.org/urn:lsid:zoobank.org:pub:9F638A1E-C17D-4A85-9D6E-3D0F24D5AE1E
The role of telomeres and telomerase in cancer and aging Meeting report of the 3rd European Workshop in Ladenburg, Germany

The maintenance of telomeres, the ends of linear chromosomes, appears to play a crucial role in senescence, aging, and cancer. The stabilization of telomere length is believed to be strongly associated with unlimited proliferation and cellular immortalization. The enzyme telomerase stabilizes telomere length by de-novo adding of telomeric repeats that had been lost by incomplete DNA replication, nucleolytic degradation, and oxidative stress. Since the telomerase is active in the majority of human tumours, thus allowing indefinite growth, it has become an attractive diagnostic and prognostic marker as well as a promising target for therapeutical intervention. Furthermore, telomerase has been talked about as a potential rejuvenation enzyme, counteracting the effects of aging. Telomere length, on the other hand, could serve as a tool for prognosis and predictive parameter in the search for the most promising approach in cancer treatment.
Epigenetics and genome stability in the human fungal pathogen Candida albicans

Large blocks of DNA repeats are commonly assembled into heterochromatin. Heterochromatic regions impose a transcriptionally repressive environment that can propagate over long distances stochastically silencing native genes as well as reporter genes inserted at these regions independently of DNA sequence. Heterochromatin, associated with repressive histone marks, not only down-regulates transcription but also inhibits recombination at repetitive elements. This epigenetic regulation could be a key regulatory step in organisms, such as microbial pathogens, that have to adapt rapidly to different environments. Here for the first time, we analysed the chromatin state of C. albicans repetitive elements and addressed whether and how this epigenetic state controls C. albicans genome stability. The results show that classic SIR2-dependent heterochromatin is assembled at the rDNA and telomeres. Interestingly, heterochromatin at telomeres is plastic and remodelled upon environmental changes. Pericentromeric regions and MRS (Mayor Repeated Sequences) are assembled into permissive chromatin bearing features of both heterochromatin and euchromatin. Surprisingly, SIR2-dependent heterochromatin does not control recombination at the rDNA. However, it inhibits recombination at the TRE (TLO Recombination Element) sequence associated with some TLO genes at subtelomeric regions. These results show that epigenetic factors promote differential genome stabitlity at different loci.
Effects of genotype on the biomechanical parameters and composition of bone in the laying hen embryos

Bone problems are highly prevalent in laying hens. These problems affect the welfare, production and economic losses. Bone development begins in the embryonic period, and if the skeletal system develops well at that time, the subsequent production period can be affected positively. The present experiment aimed to investigate the effect of genotype on biomechanical parameters and composition of bone in the laying hen embryos. For this purpose, 360 fertilized eggs were obtained from two brown (Atak-S and Brown Nick) and two white (Atabey and Nick) layer breeders and incubated. Metatarsus, tibia and femur properties were examined on the embryonic d 19 and 21. Results showed that genotype played an important role in determining the biomechanical properties and mineral composition of the metatarsus, tibia and femur in the embryonic period. Examined bone characteristics improved with embryonic age. The least mineralization was observed in the metatarsus bone. In conclusion, bone properties were infleunced from the genotype. However, these differences were not related with laying hens being white or brown. The effect of the interaction between genotype and embryonic age on the bone properties should be considered.
The effect of genetic variation and nitrogen fertilization on productive characters of Greek oregano

ABSTRACT This study aims to investigate the response of 10 Greek Oregano (Origanum vulgare subsp. hirtum) populations, collected across Greece, under 3 levels of N-fertilization during 2012 and 2013. The populations were differentiated for dry matter (from 32.7 to 63.3 g·pot−1), for essential oil content (from 2.31 to 5.86 ml·100−1 g dry weight) and for amount of essential oil (from 1.37 to 2.46 ml·pot−1), for both years. Those with the highest dry matter (1-“Palaiochori” and 5-“Gliki”) and the highest essential oil content (10-“Gytheio” and 9-“Achladocastro”) were superior by 30%, as compared to the general mean of the experiment. The populations 3-“Litochoro” and 5-“Gliki” had an increased amount of essential oil (24%) as compared to the general mean of the experiment. An additional nitrogen supply (N0 to N1 level) increased dry matter production and amount of essential oil per pot, while decreased essential oil content for all populations. Further increase of nitrogen supply, favored six populations for dry matter production and two populations for amount of essential oil per pot while had almost no effect on five populations for essential oil content. The superior populations could be used in a breeding program as starting material for the development of new cultivars.