Miracle-dz/UniFAR-FTUs huggingface dataset:
Toxoplasma gondii: parasite glycosylation and an unusual cytochrome P450 enzyme of tissue cyst-forming coccidians

Toxoplasma gondii is an apicomplexan parasite that infects approximately thirty percent of the human population. As there is a need for new therapies, it is important to investigate Toxoplasma metabolic pathways to determine their role in parasite survival. In my first project, I used metabolic oligosaccharide engineering to profile glycosylated proteins in Toxoplasma tachyzoites. This approach uses metabolic incorporation of unnatural sugars into Toxoplasma proteins. My studies identified a variety of parasite proteins that are modified by glycans and validated modification of SAG1, a surface antigen in tachyzoite stage parasites. As β-elimination reduced the modified sugar signal, Ac4GlcNAz likely targets O-linked glycans in Toxoplasma. In a second study, I characterized a novel cytochrome P450 enzyme (CYP) in Toxoplasma. TgCYP localizes to the tachyzoite mitochondrion and has an unexpectedly restricted substrate: to date, it has only been shown to act on acetone. Although tgcyp null parasites have a modest growth defect when grown in competition with wild-type parasites, the null parasites have a robust growth advantage when 2% acetone is added to the culture conditions, suggesting that expressing TgCYP is deleterious under certain conditions.
Performance of serological antibody tests for bovine tuberculosis in cattle from infected herds in Northern Ireland

The ability to accurately identify infected hosts is the cornerstone of effective disease control and eradication programs. In the case of bovine tuberculosis, caused by infection with the pathogen Mycobacterium bovis, accurately identifying infected individual animals has been challenging as all available tests exhibit less than 100% discriminatory ability. Here we assess the utility of three serological tests and assess their performance relative to skin test (Single Intradermal Comparative Cervical Tuberculin; SICCT), gamma-interferon (IFNγ) and post-mortem results in a Northern Ireland setting. Furthermore, we describe a case-study where one test was used in conjunction with statutory testing. Serological tests using samples taken prior to SICCT disclosed low proportions of animals as test positive (mean 3% positive), despite the cohort having high proportions with positive SICCT test under standard interpretation (121/921; 13%) or IFNγ (365/922; 40%) results. Furthermore, for animals with a post-mortem record (n=286), there was a high proportion with TB visible lesions (27%) or with laboratory confirmed infection (25%). As a result, apparent sensitivities within this cohort was very low (≤15%), however the tests succeeded in achieving very high specificities (96-100%). During the case-study, 7/670 (1.04%) samples from SICCT negative animals from a large chronically infected herd were serology positive, with a further 10 animals being borderline positive (17/670; 2.54%). 9/17 of these animals were voluntarily removed, none of which were found to be infected (-lesions/-bacteriology) post-mortem; 1 serology test negative animal was subsequently lesion+ and M bovis confirmed at slaughter. Importance Eradication of bovine tuberculosis (bTB; caused by Mycobacterium bovis) has remained elusive in a number of countries despite long-term coordinated test and cull programs. This can partially be explained by the limitations of available statutory tests; therefore supplementary test platforms that identify additional infected animals would be of significant utility. Overall, during our study three serological tests did not disclose a high proportion of animals as infected in high-risk cattle herds, and exhibited limited ability to disclose animals that were positive to the statutory skin test, the gamma interferon test (IFNγ), or were post-mortem confirmed with M. bovis. These serological tests could be used in a supplementary fashion to the statutory tests in particular circumstances; but may be of limited advantage where parallel use of IFNγ and skin testing is performed, as these tests together tended to disclose the majority of animals with post-mortem evidence of infection in our study cohort.
Post-fire recovery of a dryland forest remnant in the Wither Hills, Marlborough

Fire is a major threat to remnant native woody vegetation in dry, lowland New Zealand. This is because the woody flora lacks specific adaptations to survive fire, and seedling regeneration is constrained by summer drought, limited native seed rain and intense competition from non-native grasses that are often favoured by fire. In December 2000, a fire burnt a 41 ha remnant of mature Kunzea robusta (Myrtaceae) forest in the Wither Hills, Marlborough, a dry region with little remaining native woody vegetation. Shortly after the fire the area was fenced to exclude grazing animals and oversown with pasture species to stabilise the soil. A study was then initiated in June 2001 to determine the rate and direction of native forest recovery using 15 randomly located monitoring plots. Plots were re-measured in summer 2001, 2002, 2003 and 2015. Additional strategically located plots monitored the survival and re-growth of burnt individuals of Kunzea robusta, Sophora prostrata (Fabaceae) and Clematis quadribracteolata (Ranunculaceae). In spite of the dry climate, limited seed rain, oversowing and absence of grazing, woody biomass has started to recover after fire in the Wither Hills – but slowly as non-native grasses are overwhelmingly dominant. After 15 years, woody biomass and cover are less than 5% of the original estimate for the area. However, while fire-damaged Kunzea mostly died, Sophora and Clematis individuals have recovered through resprouting. Our study site is typical of many dryland areas in New Zealand in which native biodiversity is part of a productive landscape and is under threat from fire, weeds and grazing. It is inevitable that a proportion of dryland reserves will be burnt each decade and our results underscore the need for conservation planning to incorporate fire and for experimental investigations to assist with accelerating native vegetation recovery.
Hypervolume concepts in niche‐ and trait‐based ecology

Hutchinson's n-dimensional hypervolume concept for the interpretation of niches as geometric shapes has provided a foundation for research across different fields of ecology and evolution. There is now an expanding set of applications for hypervolume concepts, as well as a growing set of statistical methods available to operationalize this concept with data. The concept has been applied to environmental, resource, functional trait, and morphometric axes and to different scales, i.e. from individuals, species, to communities and clades. Further, these shapes have been variously interpreted as niches, ecological or evolutionary strategy spaces, or proxies for community structure. This paper highlights these applications’ shared mathematical framework, surveys uses of the hypervolume concept across fields, discusses key limitations and assumptions of hypervolume concepts in general, provides a critical guide to available statistical estimation methods, and delineates the situations where hypervolume concepts can be useful.
Reinterpretation of Potamogeton ×nerviger : solving a taxonomic puzzle after two centuries

Hybrids form an important component of Potamogeton diversity but their exact taxonomic identities and distributions are often insufficiently known. Potamogeton nerviger was described from Lithuania in 1827 as a proper species. Based on morphological and anatomical characters, its interpretation has since varied, ranging from synonymization with other species to identification as different hybrids and intraspecific taxa. Currently, it is universally recognized as the hybrid P. alpinus × P. lucens. Using a combined molecular, morphological and anatomical investigation we re-examined the identity of P. ×nerviger, based on both original and recent plant material. We report a successful amplification and sequencing of nuclear ribosomal ITS1 region from a 188year-old type collection. This was shown to be genetically identical to the morphologically matching plants recently collected at the type locality. Comparison with molecular characters of the possible parental species shows that P. ×nerviger is not P. alpinus × P. lucens, as currently believed, but another hybrid, P. nodosus × P. perfoliatus, which is currently called P. ×assidens. This molecular identification is also supported by anatomical evidence. In contrast, the actual existence of the hybrid P. alpinus × P. lucens is doubtful. Consequences for nomenclature and identities of records reported from other sites are discussed.
Culturing Acartia tonsa Dana and Acute Testing with Copper on Different Life Cycle Stages

Copepods are part of the zooplankton and are the biggest and most diversified group of metazoans on the earth. The huge diversity of forms, life-strategies and high sensitivity makes them the perfect candidate for ecotoxicological testing. Acartia tonsa Dana is a calanoid marine copepod with a cosmopolitan distribution that has been extensively used as a test organism. A. tonsa can survive various environmental conditions but is sensitive to a variety of toxicants. The purpose of this thesis study was to investigate the effects of acute copper toxicity on different life stages of Acartia tonsa at two different salinities. Copper was chosen as a toxicant because of the widespread distribution and its potent toxicity, despite the fact that it is an essential trace metal. A. tonsa was cultured inhouse in both 30 PSU and 15 PSU, and test individuals from the various life stages were used to perform acute toxicity tests in microwell plates. Due to lack in experience in both copepod culturing and acute testing, the results varied widely and needed to be interpreted with caution. There was no statistical difference found between 30 PSU and 15 PSU for each life stage. The following step could be chronic testing, where the data procured here forms the base. With chronic testing, the toxic effect of copper on the reproduction and development of Acartia tonsa can be investigated. There is also the possibility to use multiple toxicants to assess possible antagonistic or synergistic effects. Acartia tonsa (Dana) Acute toxicity Copper Marine Copepods Life Cycle Stages
Agrobacterium-mediated transformation of mature embryo tissues of bread wheat (Triticum aestivum L.) genotypes

Although significant progress has been made on Agrobacterium-mediated wheat transformation, current methodologies using immature embryos as recipient tissues are labor intensive, time consuming and expensive. The use of mature embryos as explants is increasingly being recognized as an optimal method for developing regenerable cell lines during wheat transformation. Therefore, we have developed an Agrobacterium-based transformation protocol using mature embryos while adjusting several factors that influence genetic transformation efficiency. In this study, we focussed on acetosyringone concentrations, genotypes and different types of mature embryos (intact or longitudinally halved-embryos or fragmented into four latitudinal pieces) used as a source of explants for the genetic transformation. A. tumefaciens strain EHA101 harboring the plasmid vector pTF101.1 carrying the barley HVA1 gene and bar-selectable marker gene were used. Mature intact-embryos and longitudinally halved-embryos yielded the highest num.
Does This Have Gluten? Comparison of Gluten-Free and Unrestricted Diets in Intestinal Bacterial Populations and Diversity

As different diets continue to grow in popularity within the United States, the effect of these diets upon bacteria in the intestines is only beginning to be understood. This study focused on the effect that a shift to a gluten-free diet has on the human gut microbiome. Three genetically close subjects were selected for observation over a six month time period. One subject observed a consistent gluten-free diet. A second subject started on an unrestrictive diet, switched to a gluten-free diet for three months, then returned to an unrestricted diet for an additional three months. The third subject left an unrestricted diet. Fecal samples were taken at set time intervals from each subject and bacterial DNA extracted. Bacterial communities were characterized by 16S rRNA gene sequencing. The subject on a consistently gluten-free diet showed a wide variation in bacterial community structure across their samples for the length of the study, while the subject on an unrestricted diet had little variation in their gut microbiome from the start to end of the study. The subject that alternated between diets showed a change in intestinal bacteria when switching to the gluten-free diet, followed by a return to something resembling the initial gut microbiome when they went back to an unrestrictive diet. However, the overriding factor was that each subject showed evidence of a characteristic gut bacterial community. This study shows that a substantial change in personal diet yields a detectable change in intestinal bacterial populations and diversity, which can then be reversed by a removal of the diet. However the individual nature of the gut microbiome means that a change in diet may not necessarily result in a gut bacterial community that resembles other individuals on that same diet.
npInv: accurate detection and genotyping of inversions mediated by non-allelic homologous recombination using long read sub-alignment

Detection of genomic inversions remains challenging. Many existing methods primarily target inversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored. We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm presence of two of these novel NAHR inversions. We show that there is a near linear relationship between the length of flanking IR and the size of the NAHR inversion.
Morphometry, allometry, and fluctuating asymmetry of egg parasitoid Trichogramma pretiosum under insecticide influence

The morphometric analysis of parasitoids may contribute to biological control programs by providing information on development of insects and relationships among sizes of morphological characters. Furthermore, it can infer about the impact of insecticides on morphological characters and fitness. We evaluate the morphometry, allometry, and fluctuating asymmetry of the egg parasitoid Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) with and without influence of the growth‐regulating insecticides teflubenzuron and lufenuron. Trichogramma pretiosum had significantly larger wings and tibiae in treatments with insecticides. We found no effects of insecticides on asymmetry in T. pretiosum and conclude that this insect is very close to isometry. This study emphasizes the importance of evaluating the size of parasitoids destined to biological control programs.
Antibacterial Activities of Rambutan Peel Extract

The antimicrobial activities of the phenolic component containing rambutan ( Nephelium lappaceum L.) extract are determined. The extract of rambutan pericarp possesses bactericidal activity against Staphylococcus aureus ATCC6538, methicillin-resistant Staphylococcus aureus (MRSA) DMST20645, and Streptococcus mutans ATCC25175T whilst no activity was found on gram negative bacteria Escherichia coli ATCC25922 and fungus Candida albicans ATCC10231 by agar disc diffusion assay. Due the rambutan pericarp extract displayed antimicrobial activity against S. aureus ATCC6538 and MRSA DMST20645 at diameter of the inhibition zone > 10 mm, tests of the minimal inhibitory concentration (MIC) of rambutan pericarp extract against S. aureus ATCC6538 and MRSA DMST20645 were further determined by broth microdilution assay resulting in 2 and 0.4 mg/ml, respectively.
Soil Heating and Secondary Plant Covers Influence Growth and Yield of Winter High Tunnel Spinach

High tunnel (HT) winter production may be limited by extreme low air temperatures, suboptimal soil temperatures, large diurnal temperature changes, and short daylengths and associated low light conditions. To determine the productivity of spinach in extreme climates, HT production trials were conducted in the fall (October to December) and winter (January to March) of 2010–12 at the Greenville Research Farm in Logan, UT (lat. 41 N. elevation 1455 m). Soil heating (±) using electric cables and secondary covers (fabric rowcovers and plastic low tunnels) were evaluated to determine combined effects on fall and winter spinach production. Soil heating signiﬁcantly increased yield in all cover treatments in the Fall 2010 (F2010) trial when spinach was planted in November, but had little to no effect on plant productivity in the other three trials (more appropriate planting dates) even though it did increase soil temperature marginally. The addition of secondary covers signiﬁcantly increased plant biomass and leaf area when compared with the uncovered control. Excluding the F2011 trial when spinach was planted earlier under more favorable temperature and light conditions, the use of low tunnels resulted in signiﬁcantly higher spinach yields (biomass and leaf area) than when grown under fabric rowcover. In the fall, relative growth rates (RGRs) decreased exponentially regardless of whether the soil was heated or not heated or if a secondary cover was used. This response was because of the seasonal decline in light levels
A new species of Paris sect. Axiparis (Melanthiaceae) from Yunnan, China

Paris Linnaeus (1573: 367) is a temperate genus of about 27 species of perennial herbs distributed in Eurasia (Li 1998, Ji et al. 2007). Most species are restricted to East Asia, chiefly to China (19 species), with the Yunnnan-Guizhou Plateau in southwest China as the centre of species diversity (Li 1998). Paris is well known in China for its medicinal value. Those species with a thick rhizome have been used as medicinal herbs for more than 2,000 years in China owing to its analgesic, haemostatic, anti-tumor, and anti-inflammatory activities (Long et al . 2003). More than 40 commercial drugs and health products have been developed in China with Paris used as raw material (Li et al . 2015).
ASSESSMENT OF CYTOTOXIC EFFECT OF METHANOLIC EXTRACTS OF LEUCAS ASPERA AND TAGETES ERECTA USING CULTURED HUMAN MONONUCLEAR CELLS

Natural products have been the most successful source of potential drug leads. Natural products have been used since ancient times and in folklore for the treatment of many diseases and illnesses. Peripheral Blood Mononuclear Cells (PBMC) was engaged for assessing the toxicity of various concentrations (100 – 500 μg/ml) of methanolic leaf extract of L. aspera and methanolic flower extract of T. erecta. Trypan blue exclusion assay was performed for different time peroid 24, 48 and 72 h. Results of the present study suggest that the lymphocytes when treated with (100 μg/ml and 200 μg/ml) L. aspera, the percentage of viability was 71.84 ± 2.91% and 66.66 ± 5.36% and 69.5 ± 0% and 66 ± 9.61% after incubating at 24 and 48 h respectively. In the case of T. erecta, percentage of cell viability upon treatment with 100 μg/ml and 200 μg/ml of methanolic extract at 24 and 48 h was found to be 90 ± 0% and 81.88 ± 0% (24 h) and 81.8 ± 0% and 81.2 ± 1.05% (48 h) respectively. Hemolysis assay was performed on red blood cells and cells treated with L. aspera extract (100 μg/ml and 200 μg/ml) did not show any increase in the absorbance at 540 nm. Whereas, cells treated with T. erecta at a 500 μg/ml exhibited only marginal increase in the absorbance value (0.246) when compared with World Journal of Pharmaceutical Research SJIF Impact Factor 7.523 Volume 6, Issue 5, 1402-1413. Research Article ISSN 2277– 7105 *Corresponding Author Dr. Arif Nisha Syad Assistant professor, PG and Research Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous). Article Received on 19 March 2017, Revised on 09 April 2017, Accepted on 29 April 2017 DOI: 10.20959/wjpr20175-8460
Identification of S-nitrosylated nuclear proteins in rat cortical neurons

The ability of neurons to modulate gene expression in response to changing environmental conditions, both during development and throughout life, is necessary for proper brain function. Although the mechanisms responsible for transducing extracellular signals into changes in gene expression remain poorly characterized, S-nitrosylation, which is the covalent attachment of a nitric oxide (NO) moiety to cysteine thiols, has been shown to be critical. In the cerebral cortex, S-nitrosylation of histone deacetylase 2 (HDAC2) is essential for gene expression during neuronal development, however few nuclear targets have been identified to date. Progress in this field of research has been hampered by the technical difficulties associated with the detection of S-nitrosylated nuclear proteins. Here, I took a novel approach by enriching for nuclear proteins of rat cortical neurons before inducing S-nitrosylation with nitrosocysteine (CysNO) and isolating S-nitrosylated proteins using S-nitrosothiol Resin Assisted Capture (SNORAC). Mass spectrometry analysis identified 614 S-nitrosylated nuclear proteins, including potential site(s) of S-nitrosylation for 67% of targets. 612 of these proteins are novel potential targets of S-nitrosylation in cortical neurons and 131 have not been shown to be S-nitrosylated in any system. Two hits, the transcription factor CREB and the histone binding protein RBBP7, were further studied and I confirmed endogenous S-nitrosylation in depolarized cortical neurons for both. In addition, I showed that CREB is S-nitrosylated at cysteines 300/310/337 located within the DNA binding domain, whereas RBBP7 is S-nitrosylated at cysteine 166, which is in a WD-repeat region that regulates protein-protein interactions. Overall, this work comprehensively identifies, for the first time, the nuclear proteins that undergo S-nitrosylation in neurons and highlights S-nitrosylation of CREB and RBBP7 as a candidate mechanism by which NO regulates gene expression in mammalian cells.
THERMAL STABILITY OF SYNTHETIC PEPTIDES MIMICKING THE SEQUENCE OF THE REGION CONTAINING THE SKIP RESIDUES IN SQUID MYOSIN ROD

Myosin is the major protein in skeletal muscles including those of fish and shellfish. The characteristics of this protein are closely related to the biological function and the quality and physical properties of muscle food. In the myosin rod (the coiled-coil region of myosin), several amino acid residues, known as skip residues, seem to destabilize the ordered structure (heptad repeat). These residues might be responsible for reducing thermal stability. Attempts were thus made to examine the role of these residues in the rod of squid myosin, based on the thermodynamic properties of synthetic peptides which have been designed to mimic the partial sequence of myosin heavy chain from the squid Todarodes pacificus mantle muscle. Five peptides, namely, with the sequence of Trp1343 -Ala1372 having the skip residue Glu1357 at the center (Peptide WT), without the skip residue (Peptide Δ), with the replacements of the skip residue (Glu) by Ile, Gln and Pro (Peptides E/I, E/Q, and E/P, respectively) to modify the helix forming propensity, were synthesized. The results obtained showed that the stability of the peptides as measured by circular dichroism spectrometry was in the order of Peptide Δ > Peptide WT > Peptide E/Q > Peptide E/P > Peptide E/I. It is suggested that the presence of the skip residues dexterously tunes the stability or flexibility of the coiled-coil structure, thus possibly regulating thick filament formation and further gel formation ability of myosin.