Miracle-dz/UniFAR-FTUs huggingface dataset:
Induced gene expression in wheat seedlings treated with a crude extract of Agapanthus africanus L. prior to leaf rust infection

It was previously shown that a crude extract of Agapanthus africanus L. (Hoffman), applied as a foliar spray to wheat ( Triticum aestivum L.) seedlings, significantly increased the in vitro activities of three pathogenesis related (PR) proteins (β-1,3-glucanase, chitinase and peroxidase). This was the case in both susceptible and resistant wheat lines whether the plants were uninfected or infected with leaf rust ( Puccinia triticina ). The aim of this study was to determine the influence of the A. africanus extract on both the intercellular PR-protein profile and PR gene expression in leaf rust infected wheat lines. Pre-treatment of infected resistant and susceptible wheat with the extract led to increased β-1,3-glucanase levels that were higher as compared to the untreated controls. Similarly, treatment with the extract led to greater expression of both the PR 3 and PR 9 genes in infected resistant and susceptible seedlings as compared to the controls. This is also applied to a retrotransposon protein encoding gene whose expression was strongly induced following extract treatment. The induced expression of all these defence-related genes suggests that the crude A. africanus extract has the ability to prime the resistance response of wheat prior to leaf rust infection. rust, induced resistance, priming, gene expression, immunoblotting, crude Agapanthus africanus extract. All Amplified cDNA fragments were cut from the agarose gel, purified using the Favorprep Gel/PCR Purification Kit (Favorgen Biotech) and re-amplified with the KAPA Taq DNA Polymerase Kit (KAPA Biosystems). The DNA fragments were sequenced using the Big Dye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) according to the manufacturer’s instructions. Sequenced fragments were ethanol-precipitated and separated on an ABI377 Sequencer (PE Biosystems). The resulting sequences were used to do a BLAST analysis (v 2.2.13) Altschul et al., 1990) with entries available on GenBank.
The true beauty of science is that it's a fantastic journey to the truth where you can stumble across some amazing surprises

2 INTRODUCTION . 3 MATERIALS & METHODS. 8 Study area . 8 Naturalistic observation and manipulation . 9 Statistical analysis . 11 Effects on males' behaviour . 12 Effects on filial cannibalism . 14 Effects on offspring survival . 14 RESULTS . 16 Fluctuations on ecological and life-history predictor variables . 16 Effects on males' behaviour . 16 Male proximity . 16 Responses to potential egg predators . 17 Effects on filial cannibalism. 22 Effects on offspring survival . 23 DISCUSSION . 27 REFERENCES . 31 Supplementary Material . 39
Further Observations and Experiments on the Cultivation of Entamoeba histolytica from Cysts

In a recent paper1, written jointly with Dr P. P. Laidlaw, methods were described for cultivating Entamoeba histolytica, and various other entozoic amoebae of man and monkeys, from the encysted forms. We there showed that cultures of all the species studied can be readily obtained by merely incubating such cysts in any of the media suitable for the cultivation of the corresponding active forms—provided that certain precautions are taken.
Farmer's perception and response towards grain-for-green program and eco-environment based on participatory rural appraisal

This paper presents an area-level analysis of farmer's perception and response towards Grain-for-Green Program and eco-environment in the loess hilly area. The analysis is based on a survey of 107 farm households by means of participatory rural appraisal. According to the nature physical conditions, such as topography, land use etc., all the surveyed farmers were divided into two groups, farmers of non-irrigated farmland and farmers of irrigated farmland, to compare their similarities and differences of perception and response towards Grain-for-Green Program and eco-environment. This paper attempted to study the issues of regional development from aspect of farmer's behavior. Based on the analysis of their behavior, some development strategies in the study region are proposed. The results indicate that most farmers' living is mainly dependent on cropland, especially for the farmers of non-irrigated farmland. The majority of farmers hold a positive attitude towards the Grain-for-Green Program. Soil and water conservation is not a conscious and voluntary behavior for farmers, but a measure to guarantee their basic agricultural production and improve their living conditions. The farmers of non-irrigated farmland prefer engineering approaches to agronomic methods because they can get much more benefits. However, the farmers of irrigated farmland pay much more attention to improve farmland quality. As far as the importance of environmental conservation is concerned, the farmers of irrigated farmland have a more favorable attitude towards it than the farmers of non-irrigated farmland. The majority of interviewees (nearly 80 per cent) consider that the local eco-environment is better than ten years before. However, nearly half of the respondents (45 per cent) never consider the environmental impact when arranging agricultural practices. Over half of the respondents (more than 55 per cent) thought that drought is the main reason of eco-environment deterioration; overgrazing and serious soil erosion is following.
Conséquences évolutives de la structuration des populations d’un ectoparasite à différentes échelles spatiales : approches empiriques sur le système puce des oiseaux-passereaux

Divergent evolution is a key process generating biodiversity. This can occur between localities, through reduced gene flow followed by local adaptation or genetic drift, and within localities through ecological specialization. In the case of multi-host parasite systems, adaptation can be driven by the relative rate of host-parasite gene flow among spatially isolated populations, and the amount of parasite exchange among local host types. Combining population genetics and field experiments, we examined how adaptation and genetic isolation shape parasite evolution. Focusing on the hen flea Ceratophyllus gallinae, a presumed host generalist, and two of its hosts, the great tit Parus major and the collared flycatcher Ficedula albicollis, we investigated parasite population structure and adaptation within a fragmented landscape. Additionally, we tested how hosts can influence encounter rates with specialized flea populations through their habitat choice. Neutral markers analyses show that flea populations are genetically differentiated at fine spatial scales, and frequently between the two host species. Evidence for parasite adaptation to each host type were also observed. Host specialization may therefore be ongoing in hen fleas. However, birds did not show specific habitat choice strategies regarding flea-infested nests. Host responses differed between two replicate sites, indicating that local population history may impact parasite evolution. Both isolation and host-based selection are therefore acting on hen flea populations at a local scale. Investigations in new localities will help to assess to what extend this divergent evolution may generate biodiversity
An Overview of Oxidative Stress and Antioxidant Defensive System

Free radicals play an important role in cell's life and death. These are unstable/unpaired electrons in their outermost shell and may become highly reactive. Reactive oxygen species (ROS) are generated from molecular oxygen/nitrogen through Electron Transport Chain (ETC), cytochrome P 450 , and other cellular and sub-cellular functions. They affect beneficial metabolic and cellular processes and also play key role in pathological conditions of the body. It is normally balanced by endogenous antioxidant system. Imbalances in redox status may develop cellular oxidative stress. If the endogenous antioxidants fail to overcome the reactive metabolites production, then exogenous antioxidants would be necessary to balance redox status. Dietary sources, including plants, herbs, spices, vitamins and herbal extracts, play an important role in this regard. This review article summarizes the functional role of Reactive Oxygen Species (ROS), reactive nitrogen species, reactive halogen species and their pathological importance. It also highlights the significant role of endogenous, as well as exogenous antioxidant system in reactive generation of intermediates.
Physicochemical controls on biogeographic variation of benthic foraminiferal test size and shape

Abstract. The sizes and shapes of marine organisms often vary systematically across latitude and water depth, but the environmental factors that mediate these gradients in morphology remain incompletely understood. A key challenge is isolating the individual contributions of many, often correlated, environmental variables of potential biological significance. Benthic foraminifera, a diverse group of rhizarian protists that inhabit nearly all marine environments, provide an unparalleled opportunity to test statistically among the various potential controls on size and volume-to-surface area ratio. Here, we use 7035 occurrences of 541 species of Rotallid foraminifera across 946 localities spanning more than 60 degrees of latitude and 1600m of water depth around the North American continental margin to assess the relative influences of temperature, oxygen availability, carbonate saturation, and particulate organic carbon flux on their test volume and volume-to-surface area ratio. For the North American data set as a whole, the best model includes temperature and dissolved oxygen concentration as predictors. This model also applies to data from the Pacific continental margin in isolation, but only temperature is included in the best model for the Atlantic. Because these findings are consistent with predictions from the first principles of cell physiology, we interpret these statistical associations as the expressions of physiological selective pressures on test size and shape from the physical environment. Regarding existing records of temporal variation in foraminiferal test size across geological time in light of these findings suggests that the importance of temperature variation on the evolution of test volume and volume-to-surface area ratio may be underappreciated. In particular, warming may have played as important a role as reduced oxygen availability in causing test size reduction during past episodes of environmental crisis and is expected to inflict metabolic stress on benthic foraminifera over the next century due to anthropogenic climate change.
Evolution of the Y Sex Chromosome in Animals Y chromosomes evolve through the degeneration of autosomes

Sex chromosomes are part of the gender determination system of many organisms. They are common in animals and rare in plants. There are many forms of sex de­ termination. Gender may be deter­ mined genetically or in response to environmental cues such as tempera­ ture or social circumstance. Genetic sex determination is typically ex­ pressed in the developing zygote but can also be mediated maternally, with some females producing only daughters and others only sons. Zygotic sex determination has ~ many forms. In bees, ants, and wasps fertilized eggs develop into females and unfertilized eggs into males. In the guppy, and many other fish, in­ vertebrates, and plants, gender is determined by the presence or ab­ sence of a sex determining gene (G, or a cluster of tightly linked genes); Gg is male and gg female. The het­ erozygous (i.e., heterogametic) sex can be female or male, depending on the species. Gender can also be de­ termined by specialized sex chromo­ somes (X and Y). In mammals, fe­ males are XX and males are XY; in birds, females are XY (sometimes designated ZW) and males are XX (sometimes designated ZZ); and in nematodes, females are XX and males are XO, in which ° denotes the absence of a homologous chro­ mosome. More than two sex chro­ mosomes are found in some species,
Sensory basis and functional role of eye movements elicited during locomotion in the land crab Cardisoma guanhumi

Eye movements in the horizontal plane and the rotatory component of body movement have been continuously recorded in land crabs, Cardisoma guanhumi Latreille, walking freely in an arena. The results show that the eyes compensate for locomotor turns by moving in the opposite direction to the body, thus reducing the image motion of surrounding objects on the retina. Gains often approach unity, so that stabilization of the rotatory component of self-generated image motion is good. Of the three compensatory eye reflexes that could contribute to these responses, optokinetic responses play a major role, since the gain of the responses of freely walking blinded crabs was about half that of crabs that could see. Since blinded crabs held above a ball moved their eyes whenever they rotated the ball about a vertical axis (i.e. turned), a significant role for leg proprioceptor-driven eye movements is also presumed. It is unclear whether vestibular nystagmus, driven by the statocysts, also has a role to play. In contrast to the high-gain compensatory responses that accompany turns, the translatory component of locomotion elicits compensatory eye movements only under the most favourable circumstances, when the crab walks along a runway facing a set of stripes. Even then, the responses are of very low gain (0.02-0.09). Amongst several possible factors, this is partly because lateral ommatidia, which drive the optokinetic responses, will face the poles of the flow field during sideways walking, and partly because stationary contrasts (as occur at the poles of the flow field) reduce the gain of optokinetic responses. It is argued that, by compensating for turns but not translatory locomotor movements, crabs effectively separate the rotatory from the translatory components of the visual flow field around them. Since only the former can be used in course control, while only the latter provides information on ground speed and the three-dimensional layout of the environment, such a separation makes good functional sense.
moveHMM: an R package for the statistical modelling of animal movement data using hidden Markov models

Due to the substantial progress in tracking technology, recent years have seen an explosion in the amount of movement data being collected. This has led to a huge demand for statistical tools that allow ecologists to draw meaningful inference from large tracking data sets. The class of hidden Markov models (HMMs) matches the intuitive understanding that animal movement is driven by underlying behavioural modes and has proven to be very useful for analysing movement data. For data that involve a regular sampling unit and negligible measurement error, these models usually are sufficiently flexible to capture the complex correlation structure found in movement data, yet are computationally inexpensive compared to alternative methods. The R package moveHMM allows ecologists to process GPS tracking data into series of step lengths and turning angles, and to fit an HMM to these data, allowing, in particular, for the incorporation of environmental covariates. The package includes assessment and visualization tools for the fitted model. We illustrate the use of moveHMM using (simulated) movement of the legendary wild haggis Haggis scoticus. Our findings illustrate the role our software, and movement modelling in general, can play in conservation and management by illuminating environmental constraints.
CHARACTERIZATION OF ADIPONECTIN AND ITS RECEPTORS IN THE CHICKEN OVARY AND TESTIS AND THEIR POTENTIAL ROLE IN CHICKEN OVARIAN TUMORIGENESIS

Adiponectin is an adipokine hormone which influences several aspects of metabolism, including glucose utilization, insulin sensitivity, lipid synthesis and energy homeostasis by signaling through two receptors, AdipoR1 and AdipoR2. A decrease in circulating adiponectin levels, as occurs in obesity in humans, has been associated with the development of insulin resistance, type 2 diabetes and tumor development. The main objectives of the current studies are: (1) To characterize the expression of adiponectin and its receptors in the chicken ovary and testis and (2) To explore their potential role in chicken ovarian tumorigenesis. RT-PCR analyses of RNA isolated from chicken follicular granulosa cells (GC) revealed the presence of AdipoR1 and AdipoR2 mRNA, while adiponectin mRNA was not detected; however, all three transcripts were found in homogenates of whole ovary. Using immunohistochemistry adiponectin-immunoreactive (ir) cells were localized to follicular theca cells (TC) but not the GC, while both AdipoR1-ir and AdipoR2-ir cells were present in TC and GC. Treatment of sexually immature chicken hens with progesterone (P4) decreased ovarian adiponectin mRNA concentration, while estradiol (E2) or P4/E2 treatment increased adiponectin mRNA expression. Estradiol treatment increased ovarian AdipoR1 mRNA quantity, while AdipoR2 mRNA quantity was not affected by any treatment. Quantitative real-time PCR (qPCR) analysis revealed T-cadherin, a putative receptor for high molecular weight adiponectin, and AdipoR1 mRNA were down-regulated in chicken ovarian tumors, while neither ovarian adiponectin nor T-cadherin protein quantities were altered by the presence of ovarian tumors, according to Western blot analysis. Using qPCR, testicular
Prognostic Power of Pathogen Cell-Free DNA in Staphylococcus aureus Bacteremia

Abstract Background Staphylococcus aureus is a leading global cause of bacteremia that can cause invasive tissue infections with high morbidity and mortality despite appropriate antibiotic therapy. Clinicians lack sufficient tools to rapidly identify patients with a poor prognosis to guide diagnostic workup and treatment decisions. Host cell-free DNA provides prognostic value across a spectrum of critical illnesses, including S. aureus bacteremia and sepsis. Metrics of high bacterial load are associated with disease severity in S. aureus bacteremia, and the objective of this study was to evaluate whether incorporating quantitation of cell-free bacterial DNA would provide additive prognostic value when combined with biomarkers of the inflammatory response. Methods S. aureus cell-free DNA was measured by quantitative polymerase chain reaction (PCR) in baseline serum samples from an observational cohort of 111 patients with complicated S. aureus bacteremia and correlated with host inflammatory markers and clinical outcomes. Results High levels of S. aureus cell-free DNA at the time of positive index blood culture were prognostic for all-cause and attributable mortality and persistent bacteremia and were associated with infective endocarditis. However, they did not provide additive value to biomarkers of the host response to infection in multivariate analysis. Conclusions Measurements of bacterial load by PCR are a clinically feasible candidate biomarker for stratifying patients at higher risk for complications and poor outcomes. Their diagnostic and prognostic value for identifying foci of infection and influencing treatment remain to be evaluated in additional cohorts.
Transcriptomic assessment of quinone mediated hepatic oxidative stress

Transcriptomic Assessment of Quinone Mediated Hepatic Oxidative Stress Joel D Parry, MRC Toxicology Unit, University of Leicester Several important anti-cancer drugs contain quinone moieties. Quinones can be chemically highly reactive and cause redox cycling, sulphydryl arylation or interact with reducing centres such as the mitochondrial electron transport chain. This chemistry maybe essential for anticancer pharmacology, but the associated toxicity also restricts use and affects development of drugs with quinone-related metabolites. Quinone based drugs are complex structures with multiple chemical properties. Therefore in this work to further understand quinone toxicity in drugs simpler structures with defined chemistry were used as tools. To discern mechanistic insight transcriptomic investigations were undertaken in rat hepatocytes and in vivo mouse liver exposed to a range of prototypical quinones. Genes important in response to quinone exposure were identified and analysed using several bioinformatic tools. Transcriptomics in hepatocytes could not differentiate quinone redox effects from other interactions, although 22 ‘quinone signature genes’ indicated a coordinated response to redox stress. A central role for mitochondria as targets of quinone interaction was confirmed, the transcriptomic profile indicating optimisation of energy metabolism and suppression of intrinsic apoptosis. Pim l and Pim3 kinases were central to this response, confirmed in follow up experiments. Pharmacokinetics from mice treated in vivo with 25mg/kg DMNQ or menadione intraperitoneally indicated DMNQ to be more widely distributed and better suited as an in vivo redox model compound than menadione. However, in vivo redox challenge from DMNQ in the liver was transient and insufficient to cause oxidative damage. The findings indicate that DM NQ has utility for studying redox stress in vivo, although a repeat dosing approach is required in future. The findings add to the knowledgebase of quinone toxicity. Particularly the increased responsiveness and sensitivity of hepatocytes in vitro compared to in vivo which may lead to an erroneous perception of toxicity if in vitro systems are studied alone.
Selenium-dependent glutathione peroxidases - A highlight of the role of phospholipid hydroperoxide glutathione peroxidase in protection against oxidalive damage

Since the discovery that selenium is an integral component of the active site of the mammalian glu-tathione peroxidase, four members of the glutathione peroxidase family have been characterised: classical cellular glu-tathione peroxidase, gastrointestinal glutathione peroxidase; plasma glutathione peroxidase and phospholipid hydroperoxide glutathione peroxidase (PHGPx) . They are products of different genes and have different specificities on hydrogen peroxide and lipid hydroperoxides, the latter are generated by free radicals and can damage cell membranes and disrupt cellular functions. Interestingly, PHGPx is not only active on phospholipid hydroperoxide, but also active on thymine hydroperoxide (a model compound for DNA damage) and protein hydroperoxides. This review highlights the role of PHGPx in protection against peroxidative damage of lipids, protein and DNA.
Advances in research on protoplast culture and fusion of woody plants

In order to conduct a comprehensive study of the present situation of protoplast culture and fusion of woody plants and to find out the low of culture, this paper dealt with the latest achievements of protoplast culture and fusion,somatic hybridization,variation selection and genetic transformation of woody plants. The technology of protoplast isolation, culture and plant regeneration were summarized. 