Miracle-dz/UniFAR-FTUs huggingface dataset:
Leveraging Transcriptomics Data for Genomic Prediction Models in Cassava

Background Genomic prediction models were, in principle, developed to include all the available marker information; with this approach, these models have shown in various crops moderate to high predictive accuracies. Previous studies in cassava have demonstrated that, even with relatively small training populations and low-density GBS markers, prediction models are feasible for genomic selection. In the present study, we prioritized SNPs in close proximity to genome regions with biological importance for a given trait. We used a number of strategies to select variants that were then included in single and multiple kernel GBLUP models. Specifically, our sources of information were transcriptomics, GWAS, and immunity-related genes, with the ultimate goal to increase predictive accuracies for Cassava Brown Streak Disease (CBSD) severity. Results We used single and multi-kernel GBLUP models with markers imputed to whole genome sequence level to accommodate various sources of biological information; fitting more than one kinship matrix allowed for differential weighting of the individual marker relationships. We applied these GBLUP approaches to CBSD phenotypes (i.e., root infection and leaf severity three and six months after planting) in a Ugandan Breeding Population (n = 955). Three means of exploiting an established RNAseq experiment of CBSD-infected cassava plants were used. Compared to the biology-agnostic GBLUP model, the accuracy of the informed multi-kernel models increased the prediction accuracy only marginally (1.78% to 2.52%). Conclusions Our results show that markers imputed to whole genome sequence level do not provide enhanced prediction accuracies compared to using standard GBS marker data in cassava. The use of transcriptomics data and other sources of biological information resulted in prediction accuracies that were nominally superior to those obtained from traditional prediction models.
Analysis of cellulose synthase genes and regulatory elements in barley and arabidopsis.

xii Statement of Authorship . xiv Acknowledgments . xvi Abbreviations . xviii General Introduction . 1 1.0 Introduction . 2 1.1 Background on Plant Cell Walls and Cellulose . 2 1.1.1 Plant Cell Walls . 2 1.1.2 Cellulose: Structure and Assembly . 8 1.2 The Genetics and Biochemical Aspects of Cellulose Biosynthesis . 14 1.2. 1 Cellulose Synthase (CesA) Genes. 14 1.2. 1.1 Dicotyledons . 15 1.2. 1.2 Monocotyledons . 16 1.2. 2 The Cellulose Synthase (CESA) Complex . 17 1.2. 3 Associated Proteins. 21 1.3 Regulation of Cellulose Biosynthesis . 22 1.3. 1 Transcription Factors Implicated in Cell Wall Biosynthesis . 23 1.4 Rationale for the Current Project . 25 1.4. 1 Application in Lodging . 26 1.4. 2 Application in Bioenergy Crops . 30 1.4. 3 Project Aims and Objectives . 32 Effects of Altering the Transcription Levels of HvCesA Genes Using the CaMV 35S Promoter . 35 2.
Dissecting the Functions of Classical Cadherins in Skin

Loss of E-cadherin has been associated with human cancers, and yet in the early mouse embryo and the lactating mammary gland, the E-cadherin null state results in tissue dysfunction and cell death. Here we targeted loss of E-cadherin in skin epithelium. The epidermal basal layer responded by elevating P-cadherin, enabling these cells to maintain adherens junctions. Suprabasal layers upregulated desmosomal cadherins, but without classical cadherins, terminal differentiation was impaired. Progressive hyperplasia developed with age, a possible consequence of proliferative maintenance in basal cells coupled with defects in terminal differentiation. In contrast, hair follicles lost integrity of the inner root sheath and hair cuticle without apparent elevation of cadherins. These findings suggest that if no compensatory mechanisms exist, E-cadherin loss may be incompatible with epithelial tissue survival, whereas partial compensation can result in alterations in differentiation and proliferation.
A novel gene organization of the rock sparrow Petronia petronia (Aves: Passeriformes) revealed by complete mitochondrial genome

Abstract The whole sequence of the Rock Sparrow (Petronia petronia) mitochondrial genome was determined using La-PCR and conserved primer walking approaches. The entire mitogenome was 17,426 bp in length and harboured 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes, and 1 noncoding control region. The mitogenome of this species resembled other avian species in gene arrangement and composition, except that tRNA-Glu had two copies and the control region contained two parts. One part of the control region is between tRNA-Glu and tRNA-Phe and a second between the two tRNA-Glu copies. The overall nucleotide composition are A (30.7%), T (23.8%), G (14.4%), and C (31.1%) with 54.5% A + T content. These mitochondrial data are potentially important for the study of molecular evolution and conservation genetics.
Improving success of rare plant seed reintroductions: a case study of Dalea carthagenensis var. floridana, a rare legume with dormant seeds

Recent reviews of rare plant reintroduction success indicate that far fewer studies have been conducted with seeds than whole plants, and of these, less than 10% have established or had long‐term population persistence reported. Because seed reintroductions are relatively less expensive than plant reintroductions, determining ways to increase efficacy of using seeds to establish rare populations has conservation benefits. In laboratory trials, we examined seed germination of an endangered legume, Dalea carthagenensis var. floridana, endemic in South Florida, U.S.A. Laboratory treatments confirmed that seeds are hard seeded, remaining viable for 1,452 days even when moist; nicking, heat, and freezing triggered higher and more rapid germination than controls. Field trials begun in 2009, using pretreated (frozen) and untreated seeds within two habitats (natural and novel) revealed that freezing pretreatment increased germination in both habitats. However, plants matured, reproduced, and established seedlings only in natural habitat, not in novel habitat. By 2012, seed treatment plots in natural pine rockland had significantly greater numbers of reproductive plants and seedlings than controls. In a restoration context, using seed pretreatments to stimulate germination can improve establishment success in suitable habitats. When paired with essential vegetation management and a controlled burn, seed augmentation helped rescue the population from the brink of extinction.
Steinernema borjomiense n. sp. (Rhabditida: Steinernematidae), a new entomopathogenic nematode from Georgia

A new species of entomopathogenic nematode, Steinernema borjomiense n. sp. , was isolated from the body of the host insect, Oryctes nasicornis (Coleoptera: Scarabaeidae), in Georgia, in the territory of Borjomi-Kharagauli. Morphological characters indicate that the new species is closely related to species of the feltiae -group. The infective juveniles are characterised by the following morphological characters: body length of 879 (777-989) μ m, distance between the head and excretory pore = 72 (62-80) μ m, pharynx length = 132 (122-142) μ m, tail length = 70 (60-80) μ m, ratio a = 26.3 (23.0-29.3), H% = 45 (40-51), D% = 54 (47-59), E% = 102 (95-115), and lateral fields consisting of seven ridges (eight incisures) at mid-body. Steinernema borjomiense n. sp. was molecularly characterised by sequencing three ribosomal regions (the ITS, the D2-D3 expansion domains and the 18S rRNA gene) and the mitochondrial COI gene. Phylogenetic analyses revealed that S. borjomiense n. sp. differs from all other known species of Steinernema and is a member of the monticolum -group.
Polysaccharides from Chinese Liupao dark tea and their protective effect against hyperlipidemia

Summary Polysaccharides-rich dark tea is believed to be beneficial to health in Southeast Asian. However, the hypolipidemic effect of Chinese Liupao tea polysaccharides (CLTPS) has not been investigated. Here, the potential mechanism by which the oral administration of CLTPS affects lipid metabolism was evaluated using high-fat diet-induced hyperlipidemia rats. In rats supplemented with CLTPS, a suppressive effect on body weight was observed after 4 weeks of intervention. CLTPS significantly improved the levels of lipid profiles, the oxidation of lipids and antioxidant enzyme activity in a dose-dependent manner. The cholesterol-lowering action was paralleled by the stimulation of cholesterol converted to bile acids along with a 1.5-fold increase in faecal excretion. Besides, the prolongation of coagulation factors and the reduction in fibrinogen content showed that CLTPS regulated the coagulation initiated through the intrinsic pathway. With current findings, CLTPS may be valuable as a natural hypolipidemic nutraceutical for human consumption.
Genetic diversity of reintroduced tree populations in restoration plantations of the Brazilian Atlantic Forest

Long‐term ecological success of large‐scale restoration programs planned for the next decades will rely on genetic diversity (GD) of reintroduced or colonizing species, a limiting factor in highly fragmented landscapes. In small and isolated natural remnants or restoration areas, substantial reduction in population's size or connectivity may lead to local extinctions due to the accumulation of deleterious recessive alleles and ongoing reduction of fecundity, plant vigor, recruitment success, and adaptive potential. Despite the paramount role of GD for species persistence, its levels in restoration programs are poorly known. We assessed the GD of four model tree species (different succession stages, dispersal, and pollination syndromes) from the Brazilian Atlantic Forest, comparing two high‐diversity restoration plantations, one forest fragment and one conserved remnant. Contrary to the expectation that the plantation strategies adopted in the restoration programs could result in genetic composition homogenization, we found that restoration areas established heterogeneous genetic groups with similar levels of neutral GD and inbreeding to those observed in natural forest remnants. This pattern was consistent across the four functionally different tree species, despite some species idiosyncrasies. For instance, we observed lower allelic richness in early successional species in restoration sites, suggesting that some species may be more prone to reintroduction with lower GD. Thus, we advocate the use of high GD levels in restoration to support biodiversity conservation in human‐modified landscapes, thus reinforcing the role of ecological restoration for recovering the diversity of genes—the basic constituent of biodiversity.
selective medium for the growth of Propionibacterium.

It PRESENTED METHOD AND MEANS FOR SELECTIVE GROWTH Propionibacterium FROM MIXED culture samples. The medium contains lactic acid SOURCE OF HEAVY METAL SALT ONE TO resistant Propionibacterium selected from A GROUP OF SALTS cadmium and arsenic water soluble.
α2B-ADRENOCEPTORS IN THE REGULATION OF VASCULAR SMOOTH MUSCLE CELL CONTRACTION AND PROLIFERATION

Anna Huhtinen α2B-Adrenoceptors in the regulation of vascular smooth muscle cell contraction and proliferation University of Turku, Faculty of Medicine, Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, Drug Research Doctoral Program and Unit of Clinical Pharmacology, Turku University Hospital, Turku, Finland. Annales Universitatis Turkuensis, Turku, Finland 2017 α2-Adrenoceptors (α2-ARs) belong to the large superfamily of G protein-coupled receptors (GPCRs). They mediate important actions of the endogenous catecholamines adrenaline and noradrenaline. All three α2-AR subtypes are involved in the regulation of blood pressure and vascular tone. α2-ARs can regulate both vascular smooth muscle contraction and remodeling of the blood vessel wall, but the intracellular signaling mechanisms involved in these functions have remained largely unknown. The aim of this thesis was to investigate the involvement of the α2B-AR subtype in the regulation of the contraction and proliferation of vascular smooth muscle cells (VSMC), and to clarify the related cellular signaling mechanisms. In order to characterize the effects of α2B-AR activation on VSMC contraction and proliferation and to investigate whether these functions could be altered by drug treatment, a VSMC line stably expressing the human α2B-AR was generated by transfection of rat A7r5 cells. Characterization of the novel A7r5-α2B cell line indicated that the localization and ligand binding properties of the expressed α2B-ARs were in line with earlier studies of α2B-ARs in different host cell environments, and that the receptors had the expected pharmacological characteristics. Therefore, the generated A7r5-α2B cell line was regarded as a useful tool for investigating the functions and regulation of α2B-ARs in VSMCs. α2B-ARs were demonstrated to be capable of mediating VSMC contraction by using a functional assay measuring myosin light chain phosphorylation, which is a biochemical readout of VSMC contraction. The network of signaling pathways involved in α2B-AR-mediated contraction of A7r5 VSMCs appeared to be complex and seemed to involve many mediators, such as Gi proteins, Gβγ subunits, phospholipase C (PLC), protein kinase C (PKC) and L-type Ca2+ channels. Different screening assays, namely DNA microarray, small inhibitor compound library screening and kinase activity profiling, were used to investigate the genetic regulation and intracellular signaling mechanisms involved in α2BAR-evoked proliferation of A7r5 VSMCs. The cellular mechanisms and signal transduction pathways participating in this response appeared to be complex and included redundancy. The employed screening assays and their respective data analysis approaches were found to be useful as tools to map the activation of cellular signaling networks in a situation where the exact mechanisms still remain unknown. These screening tools were considered suitable for hypothesis generation, but additional approaches will be required for further hypothesis testing.
Improving irrigation water management using agent technology

ABSTRACT Water use demand has increased steadily in Canterbury, New Zealand, over the last 20 years resulting in insufficient water availability. Prevailing irrigation management strategies in Canterbury consider soil moisture measurement up to a certain extent with no regard to crop’s development stages and sensitivity to water shortage; therefore, lacking to address the spatial and temporal variability of crop’s irrigation demand. This paper proposes an agent-based model that can be used to prioritise irrigation allocation to different crops on a farm. The proposed agent-based model takes into account the crop’s drought sensitivity, growth stage, soil type and the crop coefficient value when allocating water. It prioritises the crops based on their water requirements and generates an irrigation plan based on the predetermined water reduction. Our preliminary results showed that using this agent-based model, a significant water saving can be achieved even when water reduction is in effect, without impacting on production.
Novel Microsatellite Markers for Conservation of Australian Native Samadera bidwillii

Microsatellite markers were developed for Samadera bidwillii, a nationally listed vulnerable shrub or small tree, to enable investigation of its genetic structure and diversity within and among populations from its known distribution throughout coastal areas mainly in fragmented and disturbed lands from Mackay to Gympie, Queensland, Australia. The loci were tested for cross-amplification in related Samadera species. Ten polymorphic microsatellite markers were isolated and characterised from an enriched library of S. bidwillii, which exhibited di- and trinucleotide repeats. The mean number of alleles per locus ranged from 1.3 to 2.5 and mean expected and observed heterozygosities ranged from 0.06 to 0.33 and from 0.03 to 0.26, respectively in five populations. All loci successfully amplified in six other closely associated Samadera species also reported from Australia. Developed loci can be used in genetic diversity, population structure and gene flow studies with an emphasis on the conservation of S. bidwillii and related species.
A Novel Uropathogenic Escherichia Coli Genome (strain D3) and Comparative Analysis with Other Uropathogenic and Nonpathogenic Strains

Background Bacterial urinary tract infections are extremely prevalent, with half of women having at least one infection at some point in their lives. Most often the causative pathogen is the common gut microbe Escherichia coli. One such E. coli, strain D3, caused a bladder infection in a male adult, and was resistant to multiple antibiotics. We sequenced and assembled the genome of D3, and present it along with a comparative analysis against other pathogenic and nonpathogenic E. Coli strains. Results By comparing the predicted proteins of D3 with those from 5 uropathogenic and 7 nonpathogenic E. Coli strains, we generated a list of 38 genes present in most (4-5) pathogenic strains, but absent in all nonpathogenic strains. Among these were 9 proteins of the Pap fimbrial operon, which has previously been associated with cell adherence and the formation of biofilms. Lastly, we analyzed the list of predicted genes uniquely present in D3 compared to all other strains, and identified multiple transposable elements. Conclusions The presence of fimbria in most pathogenic E. coli strains, and their absence in nonpathogenic ones, suggests that they play a role in pathogenicity, a notion supported by previous work. We also found that D3-specific genes are strongly enriched with transposases, recombinases, and integrase, suggesting that these mobile elements have been inserted or expanded in D3, relative to other strains in the study.
Effect of fundectomy, antrectomy and gastrectomy on pancreatic and brush border enzyme activity in rats

on pancreatic and brush border enzyme activity in rats Summary The aim of our study was to investigate the possible effects of the removal of different parts of the stomach (fundectomy, antrectomy, gastrectomy) on the total protein content and enzyme activity in the pancreas and the brush border of the intestinal mucosa. Twenty-four 2.5-month-old male Wistar rats were divided into four groups: sham-operated animals (SHO) and those subjected to gastrectomy (Gx), fundectomy (Fx), and antrectomy (ANT). After a six-week experiment, the rats were sacrificed, and blood was collected for further gastrin analysis in serum. Samples of the pancreas, duodenum, and jejunum (proximal part in 25% of length, middle part in 50% of length, and distal part in 75% of length) were collected to determine the total protein content and enzyme activity. The rats subjected to fundectomy, antrectomy and gastrectomy showed an increased total protein content and enzyme activity (amylase, trypsin) in pancreatic tissue. They exhibited an increase in the total protein content in the homogenates of the mucosa of the proximal, middle and distal jejunum, compared to the control, and a statistical increase in maltase activity. Compared with the control group, the rats subjected to Fx and ANT showed a decreased sucrase activity in the homogenates of the mucosa of the duodenum and of the proximal, middle and distal jejunum. In the gastrectomized rats, there was a statistically significant increase in the total protein content in the homogenates of the mucosa of the jejunum, compared to the control, while the activities of lactase and sucrase were decreased. There was a statistically significant increase in the gastrin level in all experimental groups (Fx, ANT, Gx). We suggest that surgical removal of a part of the stomach radically changes the level of hormones that determine many functions of the organism. Hormonal changes may have an impact on the pancreas and the activity of brush border enzymes.
Diversity and Conservation of Waterbirds in the Northern Avifaunal Region of Sri Lanka

The aim of the present study is to evaluate the waterbird diversity, distribution, and conservation status in the northern avifaunal region of Sri Lanka, which includes two of the four richest waterbird regions in Sri Lanka, namely Jaffna and Mannar. We compiled data from the annual waterbird censuses and monthly records of the Ceylon Bird Club from 2011 to 2017 and from a systematic survey carried out by us from October 2014 to March 2016. We recorded a total of 116 species of waterbirds belonging to 23 families. Among them are species confined to the northern region including the rare breeding residents the Crab Plover ( Dromas ardeola ), Indian Courser ( Cursorius coromandelicus ), Spot-billed Duck ( Anas poecilorhyncha ), and Saunders’s Tern ( Sternula saundersi ). The Greater Flamingo ( Phoenicopterus roseus ), which is now uncommon elsewhere in Sri Lanka, was recorded in high numbers. The Spot-billed Duck, which was a very rare migrant to Sri Lanka until recently, was found to have established breeding populations in the region. The Glossy Ibis ( Plegadis falcinellus ) and Comb Duck ( Sarkidiornis melanotos ), which are extirpated breeding residents in Sri Lanka, were recorded as part of the migrant population. The Common Coot ( Fulica atra ), which was previously considered a very rare breeding resident, was found to be abundant with over 1,000 individuals in some localities.
Black spot on the medicinal orchid Dendrobium officinale caused by Cladosporium oxysporum in China

Abstract Black spot is a common disease occurring on Dendrobium officinale, which significantly reduces the quality and yield of this medicinal plant (family Orchidaceae). The disease manifests itself as small, black spots on leaves which can develop into circular streaks that become necrotic tan or brownish black, with the leaves eventually turning yellow or brown-yellow. Fungal pathogens such as Alternaria tenuissima and Phyllosticta spp. are known to cause black spot of D. officinale. A fungus which was atypical of A. tenuissima or Phyllosticta spp. was isolated from leaves of D. officinale showing symptoms of black spot from Zhejiang and Guangxi provinces, China. Pathogenicity tests in vitro as well as on tissue-cultured seedlings using fungal isolate GXDF24 showed that it was able to cause typical black spot symptoms. Molecular identification based on the ITS sequence revealed that isolate GXDF24 shared 99% similarity with Cladosporium oxysporum. This is the first report of C. oxysporum as a pathogen causing black spot of D. officinale in China.
Stability analysis for physiological traits, grain yield and its attributing parameters in oats (Avena sativa L.) in the Kashmir valley.

Eleven genotypes of oats were planted at six diverse environments to assess genotype environment interaction and determine stable oat (Avena sativa L.) cultivar in Kashmir division for grain yield using randomized block design during 2014 to 2015. There was considerable variation in grain yield and physiological traits within and across environments. Stability analysis for grain yield was conducted to check the response to Genotype x Environment interactions. The mean squares due to G x E (linear) were significant depicting genetic differences among genotypes for linear response to varying environments. Mean squares due to pooled deviations were highly significant, reflecting considerable differences among genotypes for non-linear response. Out of eleven genotypes, only three oats lines i.e., SKO-98, SKO-166 and Sabzaar, showed non-significant deviation from regression and their regression coefficient values were close to unity and desirable for grain yield across the environments. The cultivar, “SKO-98” with respective regression coefficient value of 1.018, the smallest deviations from regressions (Sdi) value (0.025) and the above average grain yield could be considered the most widely adapted cultivar.