Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of host-specific genetic markers for microbial source tracking of faecal water contamination in an agricultural catchment

Elevated nutrient concentrations in streams in the Norwegian agricultural landscape may occur due to faecal contamination. Escherichia coli (E. coli) has been used conventionally as an indicator of this contamination; however, it does not indicate the source of faecal origin. This work describes a study undertaken for the first time in Norway on an application of specific host-associated markers for faecal source tracking of water contamination. Real-time quantitative polymerase chain reaction (qPCR) on Bacteroidales host-specific markers was employed for microbial source tracking (MST) to determine the origin(s) of faecal water contamination. Four genetic markers were used: the universal AllBac (Bacteroidales) and the individual specific markers BacH (humans), BacR (ruminants) and Hor-Bac (horses). In addition, a pathogenicity test was carried out to detect the top seven Shiga toxin-producing E. coli (STEC) serogroups. The ratio between each individual marker and the universal one was used to: (1) normalise the markers to the level of AllBac in faeces, (2) determine the relative abundance of each specific marker, (3) develop a contribution profile for faecal water contamination and (4) elucidate the sources of contamination by highlighting the dominant origin(s). The results of the qPCR MST analyses indicated the actual contributions of humans and animals to faecal water contamination. The pathogenicity test revealed that water samples were STEC positive at a low level, which was in proportion to the concentration of the ruminant marker. The outcomes were verified statistically by coupling the findings of major contamination sources with observations in the field regarding local land use (residential or agricultural). Furthermore, clear correlations between the human marker and E. coli counts as well as the ruminant marker and STEC quantity in faecally contaminated water were observed. The results of this study have the potential to help identify sources of pollution for targeted mitigation of nutrient losses.
Forest pattern, climate and vulcanism in central North Island, New Zealand

A quantitative study of relationships between forest pattern and environment in the central North Island, New Zealand, is based on forest composition data from ca. 2000 existing plots distributed throughout the forests of the region. Estimates of mean annual temperature, rainfall, and solar radiation are derived for each plot from mathematical surfaces fitted to climate station data. Estimates of the depth of the last major rhyolitic eruption, (Taupo Pumice, ca. 130 AD) are derived from isopach maps. A classification procedure is used to identify broad compositional groups. Generalised linear models are used to examine relationships between major species and climatic and other physical factors. Significant relationships are identified between the distributions of both plot groups and species, and climate, vulcanism, topography and drainage. Among these factors, temperature and/or solar radiation are indicated as major determinants of the regional forest pattern, with rainfall, topography, and drainage acting at a secondary level. The role of the Taupo Pumice eruption is more difficult to interpret, and its effects seem to have been greatly influenced by topography. Deep extensive deposits of tephra on flat-to-rolling sites close to the eruption centre have probably favoured the current dominance of these sites by more rapidly dispersing conifers. In contrast, on adjacent steep sites where forest destruction was likely to be less severe, slow-dispersing Nothofagus species are largely dominant. Further work is needed to understand the factors favouring conifer dominance of the central basins and the degree to which Nothofagus species might expand their range in the future.
Forskolin Regulates Bone Sialoprotein Gene Expression in Human Breast Cancer Cells

Bone sialoprotein (BSP) is a prominent mineral-associated protein in the extracellular matrix of bone that has been implicated in the metastatic activity of cancer cells. Forskolin (FSK) is a labdanediterpene that is produced by the Indian Coleus plant. FSK elevates cyclic AMP (cAMP) via adenylate cyclase activated protein kinase A (PKA), and it is widely used to study cAMP regulation of cell processes. Here, it is reported how FSK regulates BSP gene transcription in human breast cancer MCF7 cells. FSK (1 μM) increased BSP, Runx2 and Osterix mRNA levels in MCF7 cells at 12 h. From transient transfection analyses using various BSP promoter-luciferase constructs, a cAMP response element (CRE), a runt homeodomain protein 2 (Runx2) and a fibroblast growth factor 2 (FGF2) response element (FRE) were identified as a target of transcriptional activation by FSK. Gel mobility shift analyses showed that FSK increased binding of CRE and FRE. These studies demonstrate that FSK stimulates BSP transcription in MCF7 cells by targeting the CRE and FRE elements in the BSP gene promoter.
A Preliminary Study of the Pollination Ecology of Pedicularis in the Chinese Himalaya

The pollination ecology of fourteen species of Pedicularis (Scrophulariaceae) was studied in the subalpinealpine zone of the Sichuan Himalaya. Bumblebees (Bombus Latr.) sternotribically pollinated rostrate, nectarless species with very long corolla tubes by scraping pollen. Pollinators on short-tubed, nectarless, rostrate species scraped or vibrated pollen, and nectariferous species were pollinated nototribically by nectar foragers or sternotribically by pollen foragers. Stigmas contacted residual pollen in the midline of the insect body. No evidence of lepidopteran pollination was found in any Pedicularis species. Pedicularis floral structure and function are considered to have coevolved with foraging selection by bumblebees, but pollination syndromes are not specific for a single bumblebee species nor are Bombus foragers restricted to a single plant species. Analysis of corbicular pollen loads of foragers on Pedicularis revealed a moderate degree of flower constancy, especially among foragers on nectarless flowers, probably contributing to speciation in the genus. Up to nine Pedicularis species flowered sympatrically and synchronously, and some species exhibited microhabitat selection. No putative hybrids were identified. Concepts of floral evoution in Pedicularis are in need of revision in light of new evidence presented here.
Taxonomy, phylogeny, and biogeography of the genus Oreobolus R.Br. (Cyperaceae), with comments on the biogeography of the South Pacific continents

SEBERG, O. , 1988. Taxonomy, phylogeny, and biogeography of the genus Oreobolus R.Br. (Cyperaceae), with comments on the biogeography of the South Pacific continents. The genus Oreobolus R.Br. (Cyperaceae) is revised. Fourteen species and three subspecies are recognized; two subspecies are described as new, O. obtusangulus subsp. unispicus and O. oxycarpus subsp. brownii; and a new subspecies combination is made, O. pumilio subsp. clemensiae. Comments are given on the classiciation and choice of phylogenetic and biogeographic methods. The sister-group of the genera Oreobolus and Schoenoides (which has recently been segregated from Oreobolus) is a subset of Costularia subgenus Costularia. Oreobolus is hypothesized to be monophyletic, and a phylogenetic hypothesis, based on a parsimony method, is presented. The scale-like tepals of Oreobolus are hypothesized to be apomorphic. Current vicariance biogeographic hypotheses on the relationships of the South Pacific continents are shown to be premature. Brief accounts are given on nomenclature, aspects of morphology, chromosome numbers, geographical distribution, and ecology.
Functional Analysis of the Ovarian Cancer Susceptibility Locus at 9p22.2 Reveals a Transcription Regulatory Network Mediated by BNC2 in Ovarian Cells

viii CHAPTER ONE: BACKGROUND . 1 Ovarian Cancer . 1 Ovarian Cancer Subtypes . 1 Risk Factors and Pathogenesis . 3 Genetic Predisposition to Ovarian Cancer . 5 Genome Wide Association Studies . 7 Linkage Analysis versus GWAS . 8 Principles of GWAS . 10 Caveats of GWAS . 12 Ovarian Cancer GWAS . 13 Functional Analysis of Susceptibility Loci. 16 Transcriptional Regulation . 18 Basics of Transcriptional Regulation . 18 Transcription Factor Binding . 21 Chromatin Structure . 22 3D Structure of the Genome . 24 CHAPTER TWO: IDENTIFYING FUNCTIONAL SNPS . 27 Introduction . 27 Results . 28 Candidate Functional SNPs . 28 Functional Analysis of SNPs . 31 Mapping SNPs to regulatory elements . 31 Development of Enhancer Scanning method . 33 Experimental Design . 33 Choice of template, tile verification, and host cell . 35 Controls . 36 Statistical analysis . 37 Anticipated results . 37 Limitations . 38 Mapping SNPs to regions of enhancer activity . 40 SNPs with Allele Specific Effects . 40 ii SNPs with allele specific enhancer activity . 40 Allele specific activities in electrophoretic mobility shift assays . 42 Summary . 42 Materials and Methods . 45 Candidate Functional SNPs . 45 Cell Lines and Cell Type-specific Datasets . 45 FAIRE-Seq and ChIP-Seq for Histone Modifications . 46 Enhancer Scanning . 46 Genome Browser . 48 Electrophoretic Mobility Shift Assays . 48 CHAPTER THREE: IDENTIFICATION OF TARGET GENE . 50 Introduction . 50 Results . 51 BNC2 and CNTLN as Candidate Target Genes . 51 Transcription activity at candidate gene promoters . 51 Expression Quantitative Trait Loci (eQTL). 51 Region 8 is in Physical Proximity to the TSS of BNC2 in Ovarian Cells . 58 Summary . 54 Materials and Methods . 55 eQTL Analysis . 55 3C . 55 CHAPTER FOUR: FUNCTIONAL ANALYSIS OF BNC2 . 57 Review of Basonculin 2 . 57 Identification of Basonuclin 2 and comparison to Basonculin 1 . 57 Expression of BNC2. 59 Function of BNC2 . 60 Results . 63 C2H2 Zinc Finger Proteins . 63 BNC2 Zinc Fingers Recognize Specific DNA Sequences in vitro . 65 BNC2 Genome-wide Target Sites . 68 Identification and Validation of BNC2 Target Genes . 70 BNC2 Interacts with the NuRD Complex . 75 Summary . 77 Materials and Methods . 78 Protein Binding Microarray . 78 ChIP/ChIP-Seq for BNC2 . 79 Nanostring . 82 Tandem Affinity Purification coupled to LC-MS/MS . 83 Transcriptional Repression Assay . 85 CHAPTER FIVE:DISCUSSION . 90 iii REFERENCES . 96 ABOUT THE AUTHOR . END PAGE
Genetic Variability of Rubisco in Tetraploid Wheats (Triticum turgidum)

Nineteen tetraploid wheats (Triticum turgidum), differing in their agronomical behaviour and geographic origins were grown in two experiments and analysed for the following physiological traits: soluble leaf protein content, rubisco content, initial and potential carboxylase activities of this enzyme as well as its relative content in percentage of protein, the specific activity of the enzyme and its activation state. The results show a high genetic variability for all studied traits and more particularly for the initial carboxylase activity. High phenotypic correlation was observed between the rubisco content and its potential activities, in the first experiment. Correlation between souble leaf protein and rubisco content was significant in 9 genotypes of the second experiment.
When Good Fish Make Bad Decisions: Coho Salmon in an Ecological Trap

Abstract Coho salmon Oncorhynchus kisutch are a threatened species in California. In the Shasta River, they may be caught in an ecological trap that is exacerbating their decline. Adults appear to have equal preferences for spawning habitat that reduces the survival of their young and that of apparently similar quality where survival would be more likely. The primary cause of juvenile mortality is water withdrawals, which degrade summer water quality and create barriers to movement to habitats with more suitable rearing conditions. The situation has been exacerbated by the addition of gravel to support spawning fall-run Chinook salmon O. tshawytscha, creating habitat that is also attractive to spawning coho salmon in locations where juvenile coho salmon survival will be extremely low. The Shasta River acts as a conceptual model of how habitat degradation and ecologically naive restoration actions may combine to create severe ecological traps for nontarget species. Received March 10, 2011; accepted October.
Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny

Phylogenetic relationships in the coleopteran Series Elateriformia (click beetles, jewel beetles, fireflies and allies) were investigated using > 3800 nucleotides of partial nuclear (small and large subunit rRNA genes) and mitochondrial (large subunit rRNA and cytochrome oxidase subunit I) gene sequences. The Elateriformia includes several soft‐bodied lineages, some of which retain larviform features in the adult stage (neoteny), and several major bioluminescent groups, including the families Lampyridae (fireflies), Phengodidae and Rhagophthalmidae whose relationships have been contentious. All recognized superfamilies (Elateroidea, Cantharoidea, Byrrhoidea, Buprestoidea, Dascilloidea, Scirtoidea) and 28 of the 37 families, represented in 112 individuals, were included in the analysis. Sequence alignment was based on static and dynamic homology assignments and partial removal of sequences of uncertain homology. Alignment variable regions caused a great deal of uncertainty but also contributed much of the phylogenetic signal that was insufficient to resolve deep relationships when these were removed. The main features of most analyses were the monophyly of Elateroidea + Cantharoidea (= Elateroidea sensu lato), with Omethidae + Telegeusidae frequently occupying the basal node in this group; the affinities of Dascilloidea, Buprestoidea and a (broadly paraphyletic) Byrrhoidea, with unclear relationships among them; and the monophyly of Scirtoidea (including Decliniidae) as a rather distant outgroup to all others. When mapped on the resulting trees, soft‐bodied lineages were polyphyletic, contradicting the former Cantharoidea that had been united by this trait. Transitions to neoteny were either simultaneous with, or subsequent to, the origin of soft‐bodiedness in a minimum of seven lineages. The bioluminescent groups Lampyridae (including the enigmatic genus Drilaster) and the tightly allied Phengodidae + Rhagophthalmidae were never monophyletic. The former showed close relationship to the species‐rich, soft‐bodied families Lycidae and Cantharidae, while the latter grouped with poorly resolved lineages at the base of Elateridae (click beetles). Hence, although key features as soft‐bodiedness, neoteny and bioluminescence in Coleoptera are largely confined to the Elateriformia, they appear to result from multiple origins, showing the propensity of closely related lineages to acquire similar features independently.
MIGRATING BIRDS STOP OVER LONGER THAN USUALLY THOUGHT: REPLY

The seasonal long-distance movements of migratory birds are punctuated by periods of rest and refueling termed stopovers. The duration of these periods is an important variable in the biology of migratory species. Capture-recapture provides data for the estimation of stopover duration in the many species for which individual tracking is not feasible. Schaub et al. (2001) proposed a new method for the analysis of such data. This note suggests that the method leads to erroneous estimates of mean stopover duration. Estimation of stopover duration in the absence of mortality is mathematically identical to estimation of life expectancy in the absence of emigration. Life expectancy at birth is defined as L p(a) da (1) 0 0 where survivorship p(a) is the probability of surviving at least to age a (a is continuous and p(0) 1) (Keyfitz 1985, Lotka 1998). Relating this to stopover duration, we interpret ''age'' as time since arrival, and the sur-vivorship curve p(a) as the proportion of birds remaining in the population a time units after arriving. The Cormack-Jolly-Seber (CJS) open population model (Cormack 1964, Seber 1982) provides estimates of survivorship that underlie both the analysis of Schaub et al. (2001) and this note. The stopover population is subject to recruitment and loss between samples. Stopover durations are assumed to be short, so that mortality may be ignored, and the rate of departure is given by 1 t , where t is the time-specific CJS ''survival'' parameter (probability that an animal in the population at time t will also be in the population at time t 1). Because ''survival'' is time dependent under this model, the cohort of birds arriving at time i experiences a particular ''survivorship'' curve that may be designated p i (a). In the stopover case that we Manuscript
Assessment of genomic diversity among and within Iranian confectionery sunflower (Helianthus annuus L.) populations by using simple sequence repeat markers

Abstract Genetic variation in 15 confectionery sunflower populations from different geographical regions of Iran was evaluated using microsatellites. Forty-three alleles were scored at 20 SSR loci. The average number of alleles per locus (na) and the effective allele number (ne) were 2.15 and 1.72, respectively. Observed heterozygosity (0.55) was higher than the expected (0.38) indicating lack of Hardy–Weinberg equilibrium. The genetic similarity matrix for individuals was constructed using Kosman and Leonard similarity coefficient, and Nei's Genetic Identity as well as Kosman's genetic distance was calculated among populations. Dendrograms were constructed by the unweighted pair-group method using arithmetic average (UPGMA) algorithm. The analysis of molecular variance revealed lower genetic variation among populations (14%), than within populations (86%). The average number of migrants (Nm) between populations based on AMOVA (Fst = 0.062) was 4.79. Results displayed high variation among individual plants, possibly because of the high allogamy. Genetic similarity between populations in this study could be considered as consequences of genetic equilibrium that has occurred over the long period of cultivation of confectionery sunflower in this region as well as seed exchange among provinces. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in confectionery sunflower.
Effect of dietary hydrolysate supplementation on growth performance, non-specific immune response and disease resistance of olive flounder (Paralichthys olivaceus) challenged with Edwardsiella tarda

A 9-week feeding trial was conducted to investigate the effects of dietary supplementation with protein hydrolysates on growth, innate immunity and disease resistance of olive flounder. A fishmeal (FM)-based diet was regarded as a control, and three diets were prepared by partial replacement of FM with krill hydrolysate, shrimp hydrolysate or tilapia hydrolysate (designated as Con, KH, SH and TH, respectively). Triplicate groups of fish (24.5 ± 0.3 g) were fed one of the diets to apparent satiation twice daily for 9 weeks and then challenged by Edwarsellia tarda. Fish-fed KH diet showed significantly (P < 0.05) higher growth performance and feed utilization compared with the Con diet. Dry matter digestibility of the diets was significantly increased by KH and TH supplementation. All the examined innate immune responses were significantly increased in fish fed KH diet. Significantly, higher respiratory burst and superoxide dismutase (SOD) activities were found in fish-fed SH diet. Lysozyme and SOD activities were significantly increased in fish-fed TH diet. However, no significant effect was found on fish disease resistance. This study indicates that dietary supplementation of the hydrolysates, particularly KH, can improve growth performance, feed utilization and innate immunity of olive flounder.
Copper and nickel pollution: frequency of endophytic fungi in Scots pine shoots and endophyte growth in vitro

The frequency of endophytic microfungi was measured from current-year shoots of Scots pine trees growing in Harjavalta, a heavily polluted area in western Finland. The copper (Cu) and (Ni) concentrations in bark plus phloem and needles of the same trees were measured. The frequency of isolates of endophytic taxa were either negatively (Hormonema sp. 2 and Sterile sp. 1) or positively (Hormonema sp. 1, BL132) correlated with the Cu and Ni concentration of bark plus phloem. Isolates of the most common endophytic taxa and the pathogenic Gremmeniella abietina from Harjavalta were grown in vitro in different levels of Cu (0.6 – 126 μg/mL) and Ni (0.3 – 50 μg/mL) separately and in combination. This experiment included also isolates of G. abietina and Hormonema sp. 1 from the northern (unpolluted) area. The concentrations of Cu and Ni that reduced the linear growth to 50% of control were estimated. The endophyte taxa with positively correlated frequency with increasing concentration of Cu and Ni in the shoots we.
Safflower grown in different sowing dates and plant densities

The objectives of this study were to test the effects of different plant densities on stem characteristics in two growing seasons: Fall/Winter and Spring/Summer. The plant densities evaluated were 48, 64, 80, 96, 112 and 128plants m-2. The Fall/Winter growing season was from 04/04/2008 to 23/08/2008 and the Spring/Summer growing season was from 03/10/2008 to 23/12/2008. Total and partial plant height did not differ among plant densities in the Fall/Winter growing season. However, in the Spring/Summer growing season total plant height had a quadratic response to increase in plant population whereas the partial height did not vary. In the Fall/Winter cultivation, plants presented larger stems and branches diameter, branches length and total number of nodes main stem and branches diameters, number and length of branches, fresh and dry mass decreased as density increased in the two growing seasons. The capitulum's diameter decreased as density increased in the Fall/Winter growing season, but at the Spring/Summer growing season it decreased in the density from 48 to 96plants m-2 and increased in the density from 112 a 128plants m-2.
Occupancy estimation for rare species using a spatially‐adaptive sampling design

Spatially clustered populations create unique challenges for conservation monitoring programmes. Advances in methodology typically are focused on either the design or the modelling stage of the study but do not involve integration of both. We integrate adaptive cluster sampling and spatial occupancy modelling by developing two models to handle the dependence induced by cluster sampling. We compare these models to scenarios using simple random sampling and traditional occupancy models via simulation and data collected on a rare plant species, Tamarix ramosissima, found in China. Our simulations show a marked improvement in confidence interval coverage for the new models combined with cluster sampling compared to simple random sampling and traditional occupancy models, with greatest improvement in the presence of low detection probability and spatial correlation in occupancy. Accounting for the design using the simple cluster random‐effects model reduces bias considerably, and full spatial modelling reduces bias further, especially for large n when the spatial covariance parameters can be estimated reliably. Both new models build on the strength of occupancy modelling and adaptive sampling and perform at least as well, and often better, than occupancy modelling alone. We believe our approach is unique and potentially useful for a variety of studies directed at patchily distributed, clustered or rare species exhibiting spatial variation.