Miracle-dz/UniFAR-FTUs huggingface dataset:
A Study on Antioxidant Activity of Hyptis suaveolens (L) poit

The role of free radical reactions in disease pathology is well established and is known to be involved in many acute and chronic disorders in human beings, such as diabetes, atherosclerosis, aging, immuno suppression and neuro degeneration. An imbalance between ROS and the inherent antioxidant capacity of the body, directed the use of dietary and /or medicinal supplements particularly during the disease attack. The ingestion of natural antioxidants has been inversely associated with morbidity and mortality from degenerative disorders (Halliwell et al., 1981). Antioxidant agents of natural origin have attracted special interest because of their free radical scavenging abilities (Osawa et al., 1990). The use of medicinal plants with high level of antioxidant constituents has been proposed as an effective therapeutic approach for free radical mediated diseases (Govind et al., 2011).
2D-dynamic representation of DNA/RNA sequences as a characterization tool of the zika virus genome

2D-dynamic representation of DNA/RNA sequences has been applied for the characterization of the complete genome sequence of Zika virus. Graphically, the 2D-dynamic graphs evolve with time. Numerically, applying descriptors related to the 2D-dynamic graphs, correct classiﬁcation of the sequences has been obtained. These descriptors have been shown to give an adequate characteristics of the Zika virus genome. The classi-ﬁcation diagrams form a new mathematical description of the evolution of the genome sequence of the Zika virus.
Technology-independent estimation of cell type composition using differentially methylated regions

Background High-resolution genome-wide measurement of DNA methylation (DNAm) has become a widely used assay in biomedical research. A major challenge in measuring DNAm is variability introduced from intra-sample cellular heterogeneity, which is a convolution of DNAm profiles across cell types. When this source of variability is confounded with an outcome of interest, if unaccounted for, false positives ensue. This is particularly problematic in epigenome-wide association studies for human disease performed on whole blood, a heterogeneous tissue. To account for this source of variability, a first step is to determine the actual cell proportions of each sample. Currently, the most effective approach is based on fitting a linear model in which one assumes the DNAm profiles of the representative cell types are known. However, we can only make this assumption when a dedicated experiment is performed to provide a plug-in estimate for these profiles. Although this method works well in practice, technology-specific biases lead to platform-dependent plug-in profiles. As a result, to apply the current methods across technologies we are required to repeat these costly experiments for each platform. Results Here, we present a method that accurately estimates cell proportions agnostic to platform by first using experimental data to identify regions in which each cell type is clearly methylated or unmethlyated and model these as latent states. While the continuous measurements used in the linear model approaches are affected by platform-specific biases, the latent states are biologically driven and therefore technology independent, implying that experimental data only needs to be collected once. We demonstrate that our method accurately estimates the cell composition from whole blood samples and is applicable across multiple platforms, including microarray and sequencing platforms.
Spatial and Temporal Patterns in Golden Eagle Diets in the Western United States, with Implications for Conservation Planning

Abstract Detailed information on diets and predatory ecology of Golden Eagles (Aquila chrysaetos) is essential to prioritize prey species management and to develop landscape-specific conservation strategies, including mitigation of the effects of energy development across the western United States. We compiled published and unpublished data on Golden Eagle diets to (1) summarize available information on Golden Eagle diets in the western U.S., (2) compare diets among biogeographic provinces, and (3) discuss implications for conservation planning and future research. We analyzed 35 studies conducted during the breeding season at 45 locations from 1940–2015. Golden Eagle diet differed among western ecosystems. Lower dietary breadth was associated with desert and shrub-steppe ecosystems and higher breadth with mountain ranges and the Columbia Plateau. Correlations suggest that percentage of leporids in the diet is the factor driving overall diversity of prey and percentage of other prey groups in the diet of Golden Eagles. Leporids were the primary prey of breeding Golden Eagles in 78% of study areas, with sciurids reported as primary prey in 18% of study areas. During the nonbreeding season, Golden Eagles were most frequently recorded feeding on leporids and carrion. Golden Eagles can be described as both generalist and opportunistic predators; they can feed on a wide range of prey species but most frequently feed on abundant medium-sized prey species in a given habitat. Spatial variations in Golden Eagle diet likely reflect regional differences in prey community, whereas temporal trends likely reflect responses to long-term change in prey populations. Evidence suggests dietary shifts from traditional (leporid) prey can have adverse effects on Golden Eagle reproductive rates. Land management practices that support or restore shrub-steppe ecosystem diversity should benefit Golden Eagles. More information is needed on nonbreeding-season diet to determine what food resources, such as carrion, are important for overwinter survival.
The complete mitochondrial genome of Bombax ceiba

Abstract Bombax ceiba is a beautiful and deciduous tree with important economic and ecological values. Here, we sequenced the intact mitochondrial genome (mitogenome) of B. ceiba on the PacBio sequencing platform (Pacific Biosciences, Menlo Park, CA). The mitogenome is 594,390 bp and is comprised of 35 protein-coding genes, two rRNA genes, and 25 tRNA genes. The phylogeny analysis suggested that B. ceiba was closely clustered with the genus Gossypium.
Genetic influences on B-cell function : a Dutch twin-family study

In an extended twin study we estimated the heritability of fasting HbA1c and blood glucose levels. Blood glucose was assessed in different settings (at home and in the clinic). We tested whether the genetic factors influencing fasting blood glucose levels overlapped with those influencing HbA1c and whether the same genetic factors were expressed across different settings. Fasting blood glucose was measured at home and during two visits to the clinic in 77 healthy families with same-sex twins and siblings, aged 20-45 years. HbA1c was measured during the first clinic visit. A 4-variate genetic structural equation model was used that estimated the heritability of each trait and the genetic correlations among traits. Heritability explained 75% of the variance in HbA1c. The heritability of fasting blood glucose was estimated at 66% at home and lower in the clinic (57% and 38%). Fasting blood glucose levels were significantly correlated across settings (0.34 < r < 0.54), mostly due to a common set of genes that explained between 53% and 95% of these correlations. Correlations between HbA1c and fasting blood glucoses were low (0.11 < r < 0.23) and genetic factors influencing HbA1c and fasting glucose were uncorrelated. These results suggest that in healthy adults the genes influencing HbA1c and fasting blood glucose reflect different aspects of the glucose metabolism. As a consequence these two glycaemic parameters can not be used interchangeably in diagnostic procedures or in studies attempting to find genes for diabetes mellitus. Both contribute unique (genetic) information.
The efficacy of a cultured Synergistes jonesii inoculum to control hydroxypyridone toxicity in Bos indicus steers fed leucaena/grass diets

An experiment was conducted to investigate the efficacy of a cultured Synergistes jonesii inoculum in degrading the Leucaena leucocephala (leucaena) toxins: 3-hydroxy-4(1H)-pyridone and 3-hydroxy-2(1H)-pyridone (3,4- and 2,3-DHP). Sixteen stall-housed Bos indicus steers naïve to leucaena were fed varying combinations of forage-harvested leucaena and Chloris gayana (Rhodes grass). Dietary treatments, offered at 25 g dry matter/kg LW.day, were: 25% leucaena; 50% leucaena; 100% leucaena; and 50% leucaena, switched to 50% Medicago sativa (lucerne) after 6 weeks at time of inoculation. The experiment was 10 weeks in duration, consisting of a 6-week pre-inoculation period, followed by inoculation with cultured S. jonesii, and a 4-week post-inoculation period. Mean daily dry matter intake was recorded. Twenty-four-hour urine collections and rumen fluid samples were obtained weekly for estimation of total urinary DHP, and detection of S. jonesii using nested polymerase chain reaction analysis including presence of single nucleotide polymorphisms (SNP), respectively. In the pre-inoculation period, total urinary DHP increased quickly to high levels, then gradually declined after Week 3 with 2,3-DHP the dominant isomer through to Week 6. Indigenous strains of S. jonesii were sporadically detected by PCR analysis, indicating S. jonesii was present before inoculation but at the lower limits of detection. After inoculation there was no change in the rate of total DHP degradation or the frequency of detection of S. jonesii, although there was increased rate of degradation of 2,3-DHP. SNP indicated the presence of different strains of S. jonesii in both indigenous and cultured S. jonesii. DMI was low, especially in the 100% treatment, due in part to the high stem content of the forage-harvested leucaena and probable DHP toxicosis. It was concluded that the cultured S. jonesii inoculum did not fully protect animals against leucaena toxicity.
In-Silico Analysis, Structural Modelling and Phylogenetic Analysis ofAcetohydroxyacid Synthase Gene of Oryza sativa

The Acetohydroxyacid synthase (EC 2.2.1.6) or Acetolactate synthase (ALS) belongs to a family of thiamine diphosphate (TPP) dependent enzymes which catalyzes the first reaction in the biosynthesis of essential amino acids - isoleucine, leucine and valine. Acetohydroxyacid synthase (AHAS) is present in plants, algae, fungi and bacteria and is found to be a vital target of multiple herbicides. We revealed the homology model of OsAHAS protein using the structure of Arabidopsis thaliana AHAS (PDB ID: 3E9Y) as template. The resulting model structure was refined by PROCHECK, ProSA, RMSD and Verify3D that indicated the model structure is reliable with 76% amino acid sequence identity with template. RMSD (1.75A), Verify3D (86.02%), Z-score (-9.55) and Ramachandran plot analysis showed that conformations for 81.6% of amino acid residues are within the most favoured regions. The phylogenetic tree constructed revealed different clusters based on AHAS in respect of bacteria, fungi, algae and plants. The multiple sequence alignment of these AHAS protein sequences from different organisms showed conserved regions at different stretches with homology in amino acid residues. Through motif analysis, it was revealed that conserved AHAS domain are found in all AHAS proteins suggesting its possible role in cellular and metabolic functions.
Genetic Gain of Tuber Yield and Late Blight [Phytophthora infestans (Mont.) de Bary] Resistance in Potato (Solanum tuberosum L.) Varieties in Ethiopia

Potato variety development for tuber yield and disease resistance has been conducted in Ethiopia uninterrupted since the first variety was released in 1987. However, there is an information gap about the genetic progress made over time which needs a periodic evaluation of the varieties. This study was conducted to determine the rate and magnitude of progress in tuber yield and resistance to late blight of 16 potato varieties released between 1987 and 2011 and two farmers’ varieties. The varieties were planted in randomized complete block design with three replications at Haramaya, Hirna and Arberkete in eastern Ethiopia. The analysis of variance for each location revealed the presence of significant differences among the varieties in tuber yield and resistance to late blight. The mean total and marketable tuber yields increased over locations at the rate of 0.14 and 0.18 t ha -1 , respectively, and late blight severity score reduced at the rate of 0.31% per year over the 25 years of variety development in the country. However, the increased tuber yield varied across the locations. Late blight severity score explained total tuber yield variations between 31.39 to 80.1% across the locations. It could be concluded that most of the varieties became susceptible to late blight in favourable environments for the pathogen at Haramaya and only a few varieties (Bulle, Bubu, Belete and Gera) performed better for tuber yield and late blight resistance across all locations. What is more, the varieties released recently by different centres showed higher disease severity scores than the older varieties.
Allozymic and Morphologic Differentiation between Three Ballota Species ( Labiatae ) Growing in Southern Sinai , Egypt

Ballota undulate (rare), B. Saxatilis (endangered), and B. Kaiseri (extremely endangered and endemic) are three of Mediterranean origin species grow in southern Sinai Mountains. They are very close morphologically and have been confused and mixed in their natural habitats. The present study aimed to provide genetical and morphological differentiation among the three Ballotas peceis using allozyme, PCA, and discriminant analyses for plants growing in a common environment. Electroporetic analysis of enzymes coded by 21 gene loci demonstrated that there is a high degree of genetic similarity among the three Ballota species suggesting that speciation apparently has occurred in this genus with little divergence at genes coding for allozymes. Twelve quantitative and nine qualitative characters were selected for the study of phenotypic similarity and morphological variation in a sample of 147 plants, served as OUT’s. The analyses could differentiate between B. undulata as one group and B. kaiseri and B. saxatilis as another group, but could not separate B. saxatilis from B. kaiseri. The incomplete isolation of B. undulata, B. kaiseri, and B. saxatilis, in combination with their high genetic identities and their very similar morphology, raise the question as to whether they should be retained as separate species.
The influence of the supramolecular complex PRE -1 on permeability of membranes of mitochondria

The change in the state of the mitochondrial pore of nonspecific conductivity plays a key role in the processes of triggering and regulating apoptosis. Therefore, the study of mechanisms of opening and regulating the state of these pores can have a great importance to find the ways of correcting many mitochondrial dysfunctions, including those which are associated with age-related changes. In our work, we have done a comparative analysis for swelling of brain mitochondria of adult (9 months) and mature rats (12-15 months).
Coconut (Cocos nucifera) and Moringa (Moringa oleifera) Oils Protect Against Cadmium-induced Toxicity in Albino Rats

Heavy metals are usually present in trace concentrations in different environmental matrices and exposure to these metals has become an increasing source of concern globally. Cadmium (Cd) is one of the most toxic heavy metals present in the environment due to its wide range of organ toxicity. It could be present in food, air and water where it could be ingested, inhaled or even absorbed through the skin. It has a long elimination half-life that ranges between 10–30 years. Cadmium even at low concentrations, has been shown to be highly toxic to living cells and tissues. Cadmium has no essential biological function but has been shown to negatively affect various enzymatic systems, thus has become a serious threat to living organisms. Medicinal plants are the bases of traditional medicine. The coconut (Cocos nucifera) tree is often called the “tree of life” due to its various therapeutic uses. It belongs to the Cocoideae subfamily and Arecaceae family. The oil is obtained from the kernel of Cocos nucifera and is rich in medium-chain triglycerides (MCTs). Coconut oil contains approximately, 50% of lauric acid which has potential bactericidal and viricidal actions. Coconut oil is well known for various therapeutic properties such as antioxidant, antimicrobial, antiviral and antifungal properties. Moringa oleifera is referred to as “Miracle tree”. It is native to South Asia (particularly India) but grown currently in the entire West African sub-region, Nigeria inclusive. Every part of the tree possesses some nutritional and medicinal properties. The seed and its oil, roots,
Proteolytic Processing of the Receptor-like Protein Tyrosine Phosphatase kappa and Deregulation in Human Cancer

In this thesis it is demonstrated that furin is required for constitutive processing of RPTPk within the secretory pathway. We next showed that k is specifically targeted by two additional cleavages that we named S2 and S3 to specify the result of processing at sites 2 and 3, sites downstream of S1. Processing at S2 is mediated by metalloproteases and results in RPTPk shedding. It was found to be promoted by cell density and phenothiazine exposure and ks extracellular subunit was required for shedding induced by both stimuli. Moreover, conditions that blocked the functionality of caveolae-dependent receptor internalisation into endocytic compartments diminished S2 cleavage, indicating that it proceeds in the course of internalisation via caveolae. In addition, Presenilin 1 was shown to further cleave P2, the product of S2 processing, thereby generating the cytoplasmic k isoform P3, accumulation of which is diminished by more than 90% in 10 out of 25 primary human kidney tumors. Plasminogen was identified as RPTPkMAM domain binding protein. Binding studies performed with kMAM derived peptide libraries demonstrated that Plasminogen targets the palindromic sequence DFSYLLYSQK and substitutional analysis revealed that the residues D, Y, Y and K are involved in binding. Similar motifes were identified in proteins derived from pathogenic bacteria.
Enterovirus 71 structural viral protein 1 promotes mouse Schwann cell autophagy via endoplasmic reticulum stress-mediated peripheral myelin protein 22 upregulation

Enterovirus 71 (EV71) accounts for the majority of hand, foot and mouth disease-related deaths due to fatal neurological complications. The clinical observations and animal models found the early invasion of nervous system, and the demyelinating phenomenon was observed. As one of the receptors of EV71 structural viral protein 1 (VP1), SCARB2 mainly exists on the myelin sheath. EV71 VP1 can promote viral replication through inducing autophagy in neuron cells. This study aims to investigate the role and mechanism of VP1 in autophagy of mouse Schwann cells (MSCs). An EV71 VP1-expressing vector (pEGFP-C3-VP1) was generated and transfected into MSCs. Transmission electron microscopy (TEM) and Western blot analysis of the autophagy marker microtubule-associated proteins 1A/1B light chain 3B (LC3B) were used to assess autophagy in the cells. Real-time PCR and immunofluorescent staining were performed to determine the expression of PMP22. Small interfering RNA against PMP22 was employed to investigate the role of PMP22 in MSCs autophagy. Selective endoplasmic reticulum (ER) stress inhibitor salubrinal (SAL) was employed to determine whether PMP22 is mediated by ER stress. Our results demonstrated that VP1 played a promotive role in MSC autophagy. Overexpression of VP1 upregulated PMP22. PMP22 deficiency downregulated LC3B and thus inhibited autophagy. Furthermore, PMP22 expression was significantly suppressed by SAL. VP1 promotes MSC autophagy through upregulating ER stress-mediated PMP22 expression. VP1/ER stress/ PMP22 axis in autophagy may be a potential therapeutic target for EV71 infection-induced fatal neuronal damage.
Biochemical and biophysical characterisation of the Saccharomyces cerevisiae cell-cycle transcription factors, SBF and MBF.

MBF and SBF are two large protein complexes involved in cell-cycledependent transcriptional regulation in Saccharomyces cerevisiae. These protein complexes bind to DNA sequences called MCBs {Mlu I cell-cycle box) and SCBs (Swi4/Swi6 cell-cycle box) upstream of promoters of many genes that regulate the Gl-S phase transition. The binding of MBF to MCBs and SBF to SCBs is highly regulated and requires the association of Mbplp with Swi6p (MBF), and Swi4p with Swi6p (SBF) through their C-terminal regions. This thesis describes biochemical and biophysical experiments that address crucial protein-protein and protein-DNA interactions involved in SBF and MBF-mediated regulation of the budding yeast cellcycle. Plasmids expressing various C-terminal fragments of Swi6p, Swi4p, and Mbplp, containing the heteromerisation regions, have been constructed and their respective proteins purified for structural characterisation. Initially, hydrodynamic and chemical cross-linking data suggested that a C-terminal ISkDa fragment was dimeric. This feature was later shown to be an artefact of disulphide formation in vitro. Mutation of a single conserved cysteine residue within the C-terminus of Swi6p abrogates this dimérisation, but does not show any effect on SBF-mediated transcriptional activation in vivo. The circular dichroic (CD) analyses of the Cterminal Swi6p fragments show a substantial proportion of a-helical secondary structure, verified by comparisons of CD spectra of the full-length molecule and several Nand Cterminally deleted fragments. Limited proteolysis of the 18kDa fragment suggests a bipartite helical domain within the extreme C-terminal region that is required for SBF and MBF interaction. Mutational studies of the DNA-binding region of Mbplp (1-124) that contains a winged helix-tum-helix motif suggest that the non-conserved residues C-terminal to the core domain are essential for DNA-binding. Mutations of L ysll6 (K116A) and Lysl22 (K122A) show a reduction in the apparent DNA-binding affinities for the MCB oligonucleotide duplex with respect to the wild-type protein. However, in combination, these two mutations (K116A/K122A) result in a more significant reduction in the apparent binding affinity. The results support the notion of two structurally distinct DNA-binding regions within Mbplp and related proteins.