Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and genomic analysis of small RNA pathways in nematodes

Small noncoding RNAs, including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and endogenous small-interfering RNAs (endo-siRNAs), regulate developmental and defense pathways in animals. While many small RNA silencing protein cofactors have been identified, much more is to be learned from a dynamic and quantitative perspective to reveal the underlying mechanisms and designing principles of each pathway. In this dissertation, I present studies that examine the temporal dynamics of small RNA pathways – one from an evolutionary time scale among the nematode species, and one from finely staged Caenorabditis elegans during the first larval stage. I also describe works identifying new cofactors functions in the miRNA pathway, potentially through regulating the spatial dynamics of the miRNA silencing complex. To better understand the various small RNA pathways from an evolutionary perspective, I deep sequenced small RNA from several nematode species and examined the conservation and evolution of each class of small RNAs. This reveals an extraordinary sequence fluidity of piRNAs and endo-siRNAs. However, many features such as their genomic distribution and expression patterns are highly conserved. I found that nematodes produce two distinct sex-specific classes of piRNAs, suggesting different roles for piRNAs in male and female germlines. To reveal the kinetics of miRNA-mediated silencing during the animal cell fate transition, we performed a quantitative analysis of lin-4 miRNA-mediated silencing of its target gene, lin-14. Our results point to two phases of regulation: a fast lin-14 mRNA
Using High Throughput Screens to Identify Lead Compounds for Alzheimer's Disease Therapeutics

Abstract : Alzheimer's disease (AD) is the leading cause for dementia affecting over 4.6 million people in the United States. The current FDA approved drugs only provide temporary relief from memory loss symptoms, without treating the underlying root cause of the disease. The amyloid cascade hypothesis suggests that aggregation of the amyloid beta (AB) peptide into a neurotoxic oligiomer initiates the disease. Small molecule compounds have been reported to inhibit AB peptide aggregation, as well as rescue AB induced toxicity. Screens to identify compounds are necessary to increase the chance of developing a therapeutic that prevents AB aggregation and the associated disease. Chapter 1 reviews the possible mechanism for Alzheimer's disease and discusses methods to prevent the disease. Chapter 2 presents results from an E coli based GFP fusion anti-aggregation screen. A library of 65,000 compounds was screened, and potential hits were characterized for aggregation inhibition as well as for the ability to rescue toxicity of the AB peptide Improvements to the screen are also discussed. Chapter 3 presents the results from a screen designed to identify compounds that bind to the AB peptide. Small molecule microarrays (SMM) were used to identify compounds that bind to AB. Compounds that bind have the potential of becoming aggregation inhibitors. Over 20,000 compounds were screened, and several hits from the screen are shown to rescue AB induced toxicity.
Growth of the Native Xerophyte Convolvulus cneorum L. on an Extensive Mediterranean Green Roof under Different Substrate Types and Irrigation Regimens

The possibility of using Convolvulus cneorum L. , a native Mediterranean xerophyte, with compact dome-like canopy and extended blooming period, on extensive green roofs in areas with semiarid Mediterranean climate was investigated in a 27-month experimental period, which included three summers (the dry season of the year). The aim was to preserve the local character and biodiversity, as well as to reduce water consumption and construction weight. Convolvulus cneorum rooted cuttings were planted in the beginning of July 2011 in experimental modules on a fully exposed ﬂat roof at the Agricultural University of Athens,
Labordiagnostische Referenzbereiche bei unterschiedlichen Schweinerassen sowie histopathologische und immunhistochemische Untersuchung von Gehirnen älterer Sauen und Eber auf transmissible spongiforme Enzephalopathie im Rahmen der TSE-Studie

The aim of the present study was to make a statement about selected blood ingredients for twelve pig breeds regarding the influence of the genotype. A possible race-dependence was proved for haematological parameters especially for erythrocytes, thrombocytes and leucocytes. Differences between the breeds were also found for electrolytes and the trace elements although a statement concerning breed-specifity was more difficult because some other environmental factors can have strong influence on these parameters as well. In part clear differences, which are caused by different physical characteristics and attributes of the animals such as muscle mass and susceptibility to stress, were established for substrates and enzymes. We were able to show that the pietrain pigs possess a remarkably higher concentration of some blood ingredients, in comparison with “German Landrace and Edelschwein“. To conclude, the results show, that there are marked differences in characteristics. We detected a varying influence of the genotype on the hematological and chemical blood parameters. The varying concentration of the blood parameters in the examined breeds seems to result from breed-specific metabolism and resistance to infections and environmental influence. The immune-histochemical search for accumulation of pathological prion protein with the antibody L42 in 48 brain tissue sections of both sows and boars was negativ. Nonetheless, it is possible to experimentally infect pigs with the infectious prion protein from cattle. This means that, in spite of the species-barrier, even though the infection was transmitted parenterally, pigs, along with many other animals, are susceptible to an infection with the bse-agent. There is a definite need for acquiring further knowledge on the exact onset of and events during infection and on the degree of contagiousness of transmissible spongiform encephalopathy not only in swine.
First Miocene fossils of Vivianiaceae shed new light on phylogeny, divergence times, and historical biogeography of Geraniales

The origin of Geraniales (approximately 900 species in three families: Geraniaceae, Melianthaceae, and Vivianiaceae) is traced back to the Cretaceous of Gondwana, yet their geotemporal history is largely unknown because of a limited fossil record and incomplete phylogenies. In the present study, we provide the first fossil record of Vivianiaceae and a highly resolved molecular phylogeny for all extant Geraniales genera. Our results support the hypothesis that five (instead of three) families should be recognized in the order Geraniales: Francoaceae A. Juss. (Francoa, Greyia, Tetilla), Geraniaceae Juss. (Erodium, Geranium, Monsonia, Pelargonium), Hypseocharitaceae Wedd. (monogeneric), Melianthaceae Horan. (Bersama, Melianthus), and Vivianiaceae Klotzsch (Balbisia, Rhynchotheca, Viviania). The four major lineages (i.e. Geraniaceae, Francoaceae + Melianthaceae, Hypseocharitaceae, Vivianiaceae) all originated within a narrow time frame during the Eocene (36.9–49.9 Mya) based on the five fossil calibration points. The divergence of most of the extant genera occurred much later, from the Miocene onwards. The South American–South African disjunction in Francoaceae apparently goes back to long distance dispersal with an estimated divergence time of the lineages in the Middle Miocene [11.2 (5.9–17.7) Mya]. Diversification in Melianthus appears to be much more recent than previously assumed [starting approximately 3.4 (1.9–5.2) Mya rather than approximately 8–20 Mya]. However, divergence of the Andean Hypseocharis lineage [36.9 (31.9–42.8) Mya] significantly predates the main Andean uplift: Current distributions likely go back to northward migrations and subsequent extinctions in Patagonia. Similarly, Rhynchotheca, Balbisia, and Viviania have a current southern distribution limit > 10°N of the fossil finds, indicating a massive northward displacement. The present evidence suggests that niche conservatism likely played a major role in the historical biogeography of Geraniales. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.
ROLE OF INDUCED HOST PLANT RESISTANCE IN THE MANAGEMENT OF THRIPS TABACI LINDEMAN (THRIPIDE : THYSANOPTERA) IN ONION

A Field experiment was conducted during September to December 2009 in farmers field at Karapalayam village, Tirupur district, Tamil Nadu with bulb planting of onion to study the effect of induced resistance on the incidence of Thrips tabaci (Thripidae:Thysanoptera) and occurrence of natural enemies in the onion ecosystem. The various combinations of organic nutrients such as FYM, vermicompost, neem cake, biofertilizers and Pseudomonas fluorescence were used. Among the various organics tested the combination of NPK + FYM + biofertilizers + neem cake recorded the lowest incidence of Thrips tabaci compared to the treatments receiving inorganic NPK alone. The highest bulb yield of 19.50 t/ha was obtained in the treatment where, recommended dose of inorganic nutrients was applied along with farm yard manure, biofertilizers and neem cake.
On-farm assessment of environmental and management constraints to wheat yield and efficiency in the use of rainfall in the Mallee

The responses of wheat grain yield to soil properties, weather, root diseases, and management practices were investigated in 75 grower-managed crops in the Mallee region of South Australia, Victoria, and New South Wales during 3 growing seasons. Fourteen cultivars were represented in the sampled crops, with Frame being the most common (56%). The most widespread crop sequence was wheat after pasture (43% of wheat crops), followed by wheat after fallow or cereal (both about 20%); 12% of the wheat was sown after legumes. Wheat after cereal was more common in drier sites, and wheat after fallow in wetter sites. Wheat yield was proportional to Fischer’s photothermal coefficient around flowering, and ranged from nil to 4.7 t/ha. On average, wheat crops sown after cereals yielded 0.4 t/ha less than their counterparts sown after fallow, and 0.7 t/ha less than those after legumes. Sowing date ranged from 24 April to 21 July; yield declined with delayed sowing at an average rate of 17 kg/ha.day. Growing season rainfall (April–October) ranged from 111 to 266 mm, and accounted for 27% of the variation in grain yield. Soil water content at sowing (0–1 m) ranged from 32 to 330 mm; yield increased with initial soil water at an average rate of 6 kg/ha.mm. Grain yield per unit growing season rainfall was generally low, with 75% of crops producing <12 kg grain/ha.mm; the maximum ratio was 21 kg/ha.mm. Soil constraints, including sodicity, alkalinity, salinity, and boron toxicity, reduced yield in part by reducing availability of stored soil water. Owing to severity of chemical constraints increasing with soil depth, grain yield and yield per unit growing season rainfall were both inversely related to the proportion of water stored deeper in the soil (0.5–1 m). Yield was unrelated to nitrogen, both initial and applied. Larger amounts of nitrogen accumulated in soils with more severe constraints partially accounted for the lack of association between yield and nitrogen.
Connectivity, dispersal behaviour and conservation under climate change: A response to Hodgson et al.

Summary 1. Hodgson et al. [Journal of Applied Ecology46 (2009) 964] argue that connectivity is complex and uncertain, that it can be improved incidentally by increasing habitat extent, and that connectivity conservation is unlikely to be effective under climate change. 2. We believe that they have overlooked recent research on dispersal behaviour and structural connectivity, which has improved our understanding of functional connectivity and revealed that it will not necessarily increase with habitat extent. 3. New modelling techniques including least-cost path models incorporate this more detailed understanding of connectivity into conservation planning, facilitating the true aim of connectivity conservation – to ensure appropriate interactions between habitat extent, quality and connectivity. 4. Synthesis and applications. Advances in behavioural research and modelling techniques allow us to manage structural connectivity with as much certainty as we manage extent and quality of habitat. Successful landscape conservation to address both current threats and future climate change must manage these three elements in concert.
Differential daily rhythms of melatonin in the pineal gland and gut of goldfish Carassius auratus in response to light

The objectives of this study were to test the effects of light on melatonin rhythms in the pineal gland and gut of goldfish Carassius auratus and to investigate whether melatonin function differed in these two tissues, which are photosensitive and non-photosensitive respectively. Rhythms were evaluated by measuring arylalkylamine N-acetyltransferase (AANAT2) and melatonin receptor 1 (MT-R1) mRNA expression and melatonin concentration in the pineal gland, gut (in vivo), and cell cultures of the two tissues (in vitro). Compared to control, pineal gland melatonin secretion was higher at night, whereas the 24-h dark and ophthalmectomy groups maintained higher AANAT2 and MT-R1 mRNA expression during the day. Melatonin levels and AANAT2 and MT-R1 mRNA expression in the gut were also the highest at night, but the 24-h light, dark, and ophthalmectomy groups did not significantly differ from control. Furthermore, we measured AANAT2 and MT-R1 mRNA expression in high temperature water (30 °C) to investigate differences in the antioxidant capacity of pineal gland vs. gut melatonin. Melatonin and H2O2 levels, as well as AANAT2 and MT-R1 mRNA expression, were all higher in the two tissues under thermal stress, compared with their levels at 22 °C. Taken together, our results suggest that light has no effect on melatonin patterns in the gut, which appears to exhibit its own circadian rhythm, but both gut and pineal gland melatonin exhibit similar antioxidant function.
Changes in microbial diversity associated with two coral species recovering from a stressed state in a public aquarium system

Coral diseases are a major factor in the decline of coral reefs worldwide, and a large proportion of studies focusing on disease causation use aquaria to control variables that affect disease occurrence and development. Public aquaria can therefore provide an invaluable resource to study the factors contributing to health and disease. In November 2010 the corals within the main display tank at the Horniman Museum and Gardens, London, UK, underwent a severe stress event due to reduced water quality, which resulted in death of a large number of coral colonies. Three separate colonies of two species of reef coral, Seritopora hystrix and Montipora capricornis showing signs of stress and acute tissue loss were removed from the display tank and placed in a research tank with improved water quality. Both coral species showed a significant difference in 16S rRNA gene bacterial diversity be-tween healthy and stressed states (S. hystrix; ANOSIM, R=0.44, p=0.02 and M. capricornis; ANOSIM, R=0.33, p=0.01), and between the stressed state and the recovering corals. After four months the bacterial communities had returned to a similar state to that seen in healthy corals of the same species. The bacterial communities associated with the two coral species were distinct, despite them being reared under identical environmental conditions. Despite the environmental perturbation being identical different visual signs were seen in each species and distinctly different bacterial communities associated with the stressed state occurred within them. Recovery of the visually healthy state was associated with a return of the bacterial community, within two months, to the pre-disturbance state. These observations suggest that coral-associated microbial communities are remarkably resilient and return to a very similar stable state following disturbance.
Volatiles from the burnet moth Zygaena filipendulae (Lepidoptera) and associated flowers, and their involvement in mating communication

The burnet moth Zygaena filipendulae L. contains the cyanogenic glucosides linamarin and lotaustralin, which can be degraded to the volatiles hydrogen cyanide (HCN), acetone and 2‐butanone. Linamarin and lotaustralin are transferred from the male to female during mating and thus are considered to be involved in mating communication. Because volatile semiochemical cues play a major role in mating communication in many insect species, the emissions of HCN, acetone and 2‐butanone from Z. filipendulae are characterized in the present study, aiming to determine the interplay between the degradation products of cyanogenic glucosides and pheromones. The volatile emissions from Z. filipendulae and flowers inducing mating are measured using headspace solid‐phase micro‐extraction and gas chromatography‐mass spectrometry analysis. All Z. filipendulae life stages emit HCN, acetone and 2‐butanone. Virgin females show higher emissions than mated females, whereas mated males have higher emissions than virgin males. Hydrogen cyanide is only rarely detected in the course of male–female copulation. These observations indicate a role for the cyanogenic glucoside derived volatiles in female calling and male courtship behaviours, although not as a defence during copulation. Males rejected for mating by a female are accepted after injection of linamarin or lotaustralin, demonstrating that cyanogenic glucosides are also important for female assessment of the fitness of the male. Volatiles from flowers occupied during mate calling are also analyzed, and emissions from males and females result in the identification of novel putative pheromones for Z. filipendulae.
Spatial and temporal dynamics of temperate Australian rockpool ichthyofaunas

Spatial and temporal variation, and factors influencing the structure of intertidal rockpool fish assemblages were quantitatively investigated at three large rocky headlands in south-eastern New South Wales, Australia. A total of 5244 fish from 46 species, mainly permanent intertidal residents from the families Clinidae, Blenniidae, Tripterygiidae, Gobiidae, Gobiesocidae and Girellidae, was caught in the rockpools. Numbers of species and individuals and dominance patterns of species showed significant variability within locations, possibly in response to variations in rockpool tidal height and volume, or environmental variables, such as temperature and dissolved oxygen. Species composition also differed among locations, probably as a result of availability of different habitats at each location, which may be preferred by different species. Fish assemblage structure was stable and persistent through time, presumably because rockpools are colonized only by species suitably adapted to the dynamic intertidal environment. Temporal variability in the abundance of some common species occurred during summer and autumn, mainly owing to recruitment of resident fishes. Directions for future research are given, which may contribute to an understanding of the processes that underpin these patterns.
Correlation and path coefficient analysis in five Casuarina species for productivity of biomass

In Casuarina species, character association and path coefficient analysis were worked out for 11 variables using five species in Northern dry zone of Karnataka. Genotypic correlations were higher than phenotypic correlations for all the variables. Highly significant positive correlation of biomass with tree height, clear bole height, diameter, number of branches, crown spread, volume of wood and volume index observed at both genotypic and phenotypic level. Path coefficient analysis of different traits contributing towards production of biomass yield per tree revealed that volume of wood had exercised highest direct positive effect. In similar trend direct positive effect from number of branches followed by clear bole height and diameter for biomass production was at low magnitude. However, volume index exerted negative direct effect on biomass yield per tree followed by bark thickness, needle length and crown spreading. Maximum positive indirect effect on biomass was exerted by clear bole height through volume of wood.
Extraordinarily Preserved Talpids (Mammalia, Lipotyphla) and the Evolution of Fossoriality

ABSTRACT We describe four exceptionally preserved Miocene talpid specimens from Germany (representing Mygalea jaegeri, Proscapanus sansaniensis, and Geotrypus montisasini), expanding and amending the original descriptions based on micro-computed tomography (µ-CT) data. These specimens are scored into an enlarged version of the Sánchez-Villagra et al. (2006) character set, along with newly collected data for extant talpids and the fossil species Geotrypus antiquus, Domninoides mimicus, Eotalpa belgica, and E. anglica. The extant genus Scaptonyx is here resolved as the sister taxon to the American shrew-mole, Neurotrichus, and not as a close relative of the Talpini. Of the fossil talpids, Mygalea jaegeri is recovered as the sister taxon of extant desmans only in the context of genetic constraints: morphological data alone suggest that it represents a shrew-mole/desman-grade animal. Proscapanus sansaniensis is placed at the base of the Scalopini, whereas Domninoides mimicus is the sister taxon to Parascalops and Scapanulus. Geotrypus represents an early fossorial form, with G. antiquus retaining its position at the base of the Talpini, although G. montisasini's placement remains uncertain. Interestingly, the placement of these fossils causes character states more commonly associated with the semifossorial shrew-moles to be optimized to the root of the highly fossorial Talpini. Thus, despite the close relationship between Talpini and Scalopini based on morphological data, the fossil record provides evidence to support the independent evolution of extreme fossoriality in these groups. This finding is in agreement with genetic data sets, despite obvious topological differences.
Effect of biofertilizers and inorganic fertilizers on vegetative growth and yield of okra (Abelmoschus esculentus (L.) Moench)

The present experiment was conducted at Horticultural Research Farm, Department of Applied Plant Science (Horticulture), Babasaheb Bhimrao Ambedkar University, Lucknow (U.P) during 2012-13. The experiment was conducted in a Randomized Block Design with ten treatments replicated thrice. The treatments include different biofertilizers ( Azospirillum, Azotobacterand PSB) with inorganic fertilizers (N,P,K). The results showed that application of PSB along with Azotobacter and full dose of nitrogen, potash and half dose of phosphorus resulted significantly vigorous growth and also increased yield of okra.
Correlações genéticas entre escores visuais e características reprodutivas em bovinos Nelore usando inferência bayesiana

The aim of this work was to estimate the heritability and the genetic correlations between visual scores and reproductive traits of Nelore cattle. The traits evaluated were: finishing, muscling, and conformation scores at weaning (PD, MD, and CD, respectively) and yearling (PS, MS and CS, respectively); age at the first calving (IPP) and scrotal circumference (PE). The records of 66,244 animals born between 1990 and 2006 were used. The genetic parameters were estimated using bi-trait animal analyses with Bayesian inference. A linear model for IPP and PE and a nonlinear (threshold) model for visual scores were used. The heritability estimates were: CD, 0.19±0.02; PD, 0.23±0.02; MD, 0.20±0.02; CS, 0.26±0.01; PS, 0.33±0.02; MS, 0.32±0.02; IPP, 0.16±0.03; and PE, 0.36±0.02. Genetic correlation estimates between visual scores and IPP were negative, varying from -0.18±0.03 to -0.29±0.02. Positive genetic correlations were obtained between the visual scores and PE, from 0.19±0.01 to 0.31±0.01. Animal selection with the highest visual scores, mainly those taken after the yearling age, allows to improve herd reproductive traits.