Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithms and applications of next-generation DNA sequencing : ChIP-Seq, database of human variations, and analysis of mammary ductal carcinomas

Next Generation Sequencing (NGS) technologies enable Deoxyribonucleic Acid (DNA) or Ribonucleic Acid (RNA) sequencing to be done at volumes and speeds several orders of magnitude faster than Sanger (dideoxy termination) based methods and have enabled the development of novel experiment types that would not have been practical before the advent of the NGS-based machines. The dramatically increased throughput of these new protocols requires significant changes to the algorithms used to process and analyze the results. In this thesis, I present novel algorithms used for Chromatin Immunoprecipitation and Sequencing (ChIP-Seq) as well as the structures required and challenges faced for working with Single Nucleotide Variations (SNVs) across a large collection of samples, and finally, I present the results obtained when performing an NGS based analysis of eight mammary ductal carcinoma cell lines and four matched normal cell lines.
Intraspecific Morphological Variability in Megalopae of Three Sympatric Species of the Genus Cancer (Brachyura: Cancridae)

ABSTRACT Selected morphological traits were documented for megalopae of Cancer magister, C. oregonensis,and C. productus collected at three sites within the Puget Sound basin and at two offshore sites in the eastern Pacific Ocean. Variation in selected traits was compared among species, among individuals within species, and among regions sampled. Traits selected for measurement were those proposed in the literature as diagnostic for identification of species of Cancer. For each of three species of Cancer collected, substantial intraspecific variability in size and appendage setation was documented. Although individual megalopae differed in selected morphological traits from published reports, published values were within the range of those measured in the present study. Significant differences among regions were determined for size and setation in C. magister, with the clearest differences being those between megalopae collected offshore and within the Puget Sound basin. Results indicate that megalopae of C. magister can be separated from those of C. productus and C. oregonensis by size alone, but that the latter two species cannot be separated with certainty on the basis of features described in the literature as diagnostic. Differences between offshore and inland water populations of megalopae of C. magister may reflect hydrographic features of the region and the megalopa's site of origin. Variability in morphological traits must be included in any analysis of factors for species identification and may contribute to analysis of broader ecological issues.
Assessing Microplastic Pollution in Four Mile Run, an Urban Stream in Northern Virginia

Microplastics are pollutants of concern in waterways and oceans for their persistence and impact on aquatic life and food webs. This study demonstrates a low-cost land-based sampling method to assess the extent of microplastic pollution found in Four Mile Run, an urban stream in Northern Virginia. Microplastic particle counts in environmental and treated wastewater ranged from 0.01-0.24 particles L-1 (mean 0.08 particles L-1) and from 2 to 446 μg L-1 (mean 70 μg L-1), with fibers found to be the most common microplastic category. Treated wastewater effluent was found to be a significant source of microplastic pollution, though microplastics were also found upstream of any influence from wastewater or tide-borne materials. The sampling method proved effective for collecting and analyzing microplastic pollution, though the sample size of 100 L was deemed insufficient for reliable measurement of total mass of microplastics.
Clathrin is required for Scar/Wave-mediated lamellipodium formation

The Scar/Wave complex (SWC) generates lamellipodia through Arp2/3-dependent polymerisation of branched actin networks. In order to identify new SWC regulators, we conducted a screen in Drosophila cells combining proteomics with functional genomics. This screen identified Clathrin heavy chain (CHC) as a protein that binds to the SWC and whose depletion affects lamellipodium formation. This role of CHC in lamellipodium formation can be uncoupled from its role in membrane trafficking by several experimental approaches. Furthermore, CHC is detected in lamellipodia in the absence of the adaptor and accessory proteins of endocytosis. We found that CHC overexpression decreased membrane recruitment of the SWC, resulting in reduced velocity of protrusions and reduced cell migration. By contrast, when CHC was targeted to the membrane by fusion to a myristoylation sequence, we observed an increase in membrane recruitment of the SWC, protrusion velocity and cell migration. Together these data suggest that, in addition to its classical role in membrane trafficking, CHC brings the SWC to the plasma membrane, thereby controlling lamellipodium formation. Introduction Lamellipodia are protrusions of the plasma membrane that define a leading edge during cell migration (Abercrombie et al., 1970). The membrane is projected through the force provided by actin polymerisation, which can be mainly ascribed to the activity of the Arp2/3 complex that generates branched actin networks (Pollard, 2007). In mammalian cells, the three Wave proteins have emerged as the major activators of the Arp2/3 complex at The small GTPase Rac controls lamellipodium formation through Wave proteins (Miki et al., 1998). Wave proteins are embedded into multiprotein complexes, the purification of which provided the molecular link between the like Wave proteins, most subunits of the Wave complex are encoded by paralogous genes, which are variably expressed in different cell types, giving rise to a combinatorial complexity of the Wave complexes that can be assembled (Derivery and Gautreau, 2010). The most ubiquitous Wave complex is composed of Sra1, Nap1, Abi1, Brk1 and Wave2 (Gautreau et al., 2004).
IMPACT OF THE IMPORTED FIRE ANT ON LABORATORY POPULATIONS OF COTTON APHID (APHIS GOSSYPII) PREDATORS

The presence of a few red imported fire ants, Solenopsis invicta Buren, workers on aphid bearing cotton plants reduced aphid predator effectiveness in the laboratory. The predators Hippodamia convergens Guerin-Meneville adults and 3rd instar larvae were effective in reducing Aphis gossypii Glover populations as did 3rd instar larval Chrysopa carnea Stephens, Scymnus louisianae Chapin and Syrphus sp. larvae. However, all of these predators were ineffective in the presence of fire ants which were capable of killing all species although both Scymnus and Syrphus larvae sometimes escaped. Although predators may be killed they may prefer areas of low ant encounters in the field thus surviving and reducing their impact on fire ant tended aphid populations.
Occurrence and removal of Giardia and Cryptosporidium at the Goreangab Reclamation Plant

This paper deals with the occurrence of Giardia and Cryptosporidium in the water sources available for the Goreangab Reclamation Plant (GRP) and the subsequent removal during treatment at the reclamation plant. Giardia is detected more often than Cryptosporidium. 60% of the time it is detected in the samples from the dam and in 55% of the samples from the maturation pond effluent. During the investigation, Giardia was detected in the final water 5% of the time and Cryptosporidium 2% of the time. The maximum Giardia cysts detected in a sample was 30, the 99% percentile was 20 and the 97% percentile 10 cysts. A maximum of 20 Cryptosporidium oocysts was detected in a sample. The 99% percentile counted 6.2 oocysts arid the 97% percentile 0 oocysts. From the data presented it is clear that the polluted dam water has the same risk level of Giardia and Cryptosporidium pollution as treated wastewater effluent. This emphasises the fact that the sources should be monitored continuously for these parasites. The sporadic high counts of Giardia and Cryptosporidium in the raw water sources indicate that a multiple-barrier approach must be followed to ensure the safe operation of even conventional treatment plants using polluted source water. No correlation could be found between cyst and oocyst removal and other water quality parameters. The advocating of a final water turbidity ol 0.1 NTU and the use of particle counters can only be supported by these findings, as it is possible to achieve a turbidity of less than 0.1 NTU at the sand filter outlet, even in a developing country like Namibia. The challenge lies with the maintenance of equipment and vigilance of the operators.
GEOTECHNICAL CHARACTERISATION OF THE MIOCENE

9 The design of complex underground structures in an urban environment requires in the first instance 10 an appropriate characterisation and interpretation of the ground conditions and of the mechanical 11 behaviour of soil formations in the ground profile. With such information it is then possible to select 12 and calibrate appropriate soil constitutive models for application in advanced numerical analysis, with 13 the objective of predicting the induced ground movements and the potential damage to existing 14 structures and services. This paper provides an interpretation of the site investigation data collected 15 for the numerical analysis and design of the Ivens shaft excavation in Lisbon, Portugal. For the first 16 time a comprehensive set of interpreted data is obtained for two of the main formations in the Lisbon 17 area, Argilas e Calcários dos Prazeres (AP) and Areolas da Estefânia (AE), improving the understanding 18 of their mechanical behaviour and making the data available for application in most soil constitutive 19 frameworks. It is evident from the results that even with careful testing procedures the data may 20 appear to be inconsistent, requiring further assumptions when deriving soil parameters. Such 21 assumptions are discussed and an emphasis is placed on the need to combine data from laboratory 22 and field investigations. 23 24
Fruit anatomy of some Apiaceae plant species from Niğde- Aladağlar/ Turkey

Anatomical characters are very important to distinguish between closely related species and genera, especially in the family Apiaceae. Anatomy of Apiaceae fruits varies strongly, even among closely related species in the same genus. An ethnobotanical study was conducted between 2004 and 2005 in order to determine wild used plants in West part of Nigde-Aladaglar. According the data of this study's, 3 plant species belong to Apiaceae family sold to different tea companies by local people. Anatomical characteristics of fruits of the Ferulago pachyloba, Prangos ferulacea, Prangos meliocarpoides have been studied. Ferulago pachyloba has winged dorsal ribs, equal to or shorter than seeds. Prangos ferulacea has five blocks of mesocarp, they are not separated by the exocarp and the vascular bundles usually surround each block. Prangos meliocarpoides has continuous mesocarp and not separated into blocks. Druse crystals do not exist in the endosperm of F. pachyloba, P. ferulacea, and P. meliocarpoides.
Molecular cloning and expression analysis of a WRKY transcription factor in sugarcane

The WRKY proteins comprise a superfamily of transcription factors which are unique in plants. In the present study, a WRKY gene of sugarcane was isolated. This gene is 1 003 bp in full length, which includes 93 bp 5’ untranslated region (UTR) and 172 bp 3’ UTR. The open reading frame (ORF) of this gene is 738 bp which encodes 245 amino acids, with a typical WRKY DNA-binding domain at the 127 ~ 186 aa of the deduced amino acid sequences. The cysteine and histidine are also rich at the 153 ~ 184 aa, which is a C2H2 zinc finger domain of Class II and located at the C-terminal end of this deduced amino acid sequence; thus, this gene belongs to WRKYII. Furthermore, the prokaryotic expression vector of Sc-WRKY gene was successfully constructed and expressed in Escherichia coli (BL21 strain), and the molecular weight of the targeted product was about 25.7 kD. Real-time quantitative PCR analysis demonstrated that the Sc-WRKY gene was strongly induced by Ustilago scitaminea, salicylic acid (SA), NaCl and PEG, which suggests that this gene might play an important role in smut-resistant, drought-tolerant and salt-tolerant mechanism.
The effect of the zoo setting on the behavioural diversity of captive gentoo penguins and the implications for their educational potential

Investigations into the effect of the captive environment on zoo and aquarium-housed animals is now a well-established area of research, yet little attention is given to the effect of these animals on zoo visitors. It has been suggested that some animals have a greater ability to attract and thus educate visitors, but there is a dearth of information in this area. Furthermore, before a captive species’ educational potential can be determined, its response to the zoo environment should be investigated to ensure its welfare. The current study first considered the effect of visitor presence and environmental enrichment on the behavioural diversity levels of aquarium-housed gentoo penguins ( Pygoscelis papua ), with particular attention given to pool-use and nesting behaviour. Then, based on the animals’ response to the visitors and enrichment, we consider the educational potential of the penguin group. Data were obtained through scan samples taken throughout the breeding season. Results indicate that visitor number affects behavioural diversity levels, with higher numbers of visitors associated with greater behavioural diversity and pool use by penguins. However, neither visitor behaviour nor enrichment appeared to affect behavioural diversity. Nesting behaviour was not affected by any of the variables that were tested. Based on these results we conclude that the penguins at this aquarium have a high educational potential. The results of this study suggest that future research should consider the use of interactive enrichment and how captive penguins may further enhance visitor learning.
Impact of a tannin extract on digestibility, ruminal fermentation and duodenal flow of amino acids in steers fed maize silage and concentrate containing soybean meal or canola meal as protein source

SUMMARY Four Holstein steers (297 ± 56 kg of body weight (BW)) fitted with duodenal cannula and rumen catheter, were housed in metabolism cages and used in a 4 × 4 Latin Square trial to evaluate the effect of both protein source and Acacia mearnsii tannin extract on digestibility, ruminal fermentation, rumen microbial protein synthesis, N utilization and on duodenal flow of individual amino acids. The diet was offered at restricted amount of 25 g of dry matter (DM)/kg BW and consisted of maize silage plus concentrate, in a proportion of 0·7:0·3 (DM basis) respectively. Concentrate was formulated with either soybean meal or canola meal as protein source, with or without 50 g/kg of A. mearnsii tannin extract (i.e. 15 g/kg of total dietary DM). There was no effect of protein source on most variables. The apparent and true organic matter (OM) digestibilities, as well as neutral detergent fibre (NDF) digestibility were negatively affected by tannin extract inclusion without, however, affecting digestible OM intake. The amount of nitrogen (N) excreted in faeces increased whereas the urinary N excretion decreased in tannin extract treatments. No interaction time × treatment was detected for any rumen variable and no treatment effect was observed for rumen fluid pH and reducing sugars concentration. Rumen fluid concentration of ammonia N was lower for the canola meal plus tannin extract treatment. Rumen concentration of α-amino compounds was not affected by tannin extract but was higher when canola meal was the protein source. The duodenal flow of OM, total N, α-amino N and non-ammonia non-microbial N increased with tannin extract inclusion, whereas the duodenal flow of microbial N was not affected by treatment. For both protein sources, the amount of most individual amino acids flowing to the duodenum increased due to tannin extract addition. In conclusion, the dietary inclusion of 15 g/kg DM of tannin extract from A. mearnsii improved the amino acid supply independently of whether the protein source was canola meal or soybean meal, without affecting the amino acid profile, to steers fed maize silage plus concentrate, with a minor but significant impact on OM digestibility.
Hydraulic Resistance of Plants. I. Constant or Variable

Two popular equations for describing the flow of water through plants are discussed and criticized. They are the Ohm's Law analogue, in which the flow rate is assumed to be proportional to the difference in water potential across the plant, between leaf and soil; and an equation, used widely to describe transmembrane fluxes of single cells, in which the flow rate is assumed to be the sum of two components, one proportional to the difference in hydrostatic pressure, the other proportional to the difference in osmotic pressure, between specified points in the plant. The well-established theoretical inadequacies of the Ohm's Law analogue are reviewed, especially the poorly recognized fact that it is of little use if substantial amounts of solutes are flowing with the water. The other, composite, equation does not have the same grave theoretical inadequacies, but its failure to agree with published data is highlighted.
Ecology and Behavior of the Gila Monster in Southwestern Utah

Activity patterns, behavior, food habits, and thermal biology were investigated by radio- telemetry in a population of banded Gila monsters in southwestern Utah. Twenty-seven Gila monsters were observed within a 2 km2 area. They fed on eggs and young mammals taken from nests. Quantities as large as 210 g, eaten in a single meal, did not appear to be envenomated. Activity peaked between late April and mid June, from 0800 to 1200 h. Distances traveled during activity bouts averaged 210 m (ap- proximately 50 min), although individuals occasionally traveled over 1 km. Lizards were active on less than 10 days/month during their 90-day activity season, spending over 95% of their time below ground in shelters. This low energetic investment to activity is contrary to traditional descriptions of activity of lizards that forage on patchy prey. Gila monsters had a relatively low activity temperature (x = 29.4 C) and at rest spent over 83% of the year at body temperatures of 25 C or below. Lizards occasionally basked near shelters in the spring. Several shelters were reused, some by more than one lizard, occasionally concurrently. Intraspecific interactions, including male combat, observed near shelters suggest that these helodermatids have a structured social system. Analysis of a 3-h fight between two large males revealed similarities with varanid lizard and crotaline snake combat, as well as similarities to combat in captive helodermatids.
A New Phenylpropanoid Glycoside from Tibetan Folk Drug Pulicaria insignis

In order to investigate the bioactivity constituents of Tibetan folk drug Pulicaria insignis,four compounds were isolated with chromatography techniques.Structures were elucidated to be 2,4-dihydroxy-6-methyl-ethanone-4-O-β-D-Glc(1),4-(3'-hydroxypropyl)-2,6-dimethoxyphenol-3'-O-β-D-glcoside(2),4-allyl-2-methoxyphenol-1-O-β-D-glcoside(3),2-methyl-1,3,6-trihydroxy-9,10-anthraquinone-3-O-(6'-O-Ac)-α-L-Rha-(1→2)-β-D-Glc(4)on the basis of spectroscopic analysis including 1D,2D-NMR,MS and HRMS.Four compounds were isolated from the genus Pulicaria for the first time.2,4-Dihydroxy-6-methyl-ethanone-4-O-β-D-Glc(1)is a new phenylpropanoid glycoside.
Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median FST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.
Effects of sudden salinity changes on short-term hematological and biochemical responses in Mudskipper Periophthalmus waltoni Koumans 1941 (Gobiidae: Perciformes)

The present study investigates and reports the effects of sudden salinity changes on short-term hematological and biochemical responses in Walton's mudskipper, Periophthalmus waltoni . For this purpose, mudskippers caught from coastal area of Persian Gulf (Bandar Khamir, Hormozgan Province, Iran) were acclimated and fed with frozen blood worms ( Chironomus ) for one month prior to the start of experiments. After acclimation, groups of 15 individuals were fully submerged in either dechlorinated tap water (fresh water; Group A), 50% seawater (SW) (17‰ salinity; Group B), or 100% SW (35‰ salinity; Group C) during a period of 24 hours. Fish which were free to be in or out of 50% SW served as controls. Statistical analysis showed a significant influence of salinity levels on erythrocyte, haemoglobin, haematocrit, leucocytes, lymphocytes, neutrophils, monocytes and on all biochemical parameters tested during the study. It seems that the changes recorded in haematological and biochemical parameters were the best strategy that the Walton's mudskipper has to adapt itself to an environment with different salinity levels.