Miracle-dz/UniFAR-FTUs huggingface dataset:
Seedbank-Vegetation Relationships in Restored and Degraded Annual California Grasslands: Implications for Restoration

Seedbanks represent the pool of species that could germinate and establish into plant communities. Seedbank analysis complements vegetation monitoring and has direct applications for restoration. For most restoration projects, viable seeds of planted species must be present in the seedbank for these species to persist. Degraded California grasslands are increasingly restored to reverse widespread loss of these iconic habitats that support numerous species and provide critical ecosystem services. We analyzed seedbank composition and seedbank-vegetation relationships in paired restored and unrestored Central Valley grasslands to determine: 1) if seeded grasses had persisted in seedbanks and/or vegetation; 2) if native grasses were still present in seedbanks and/or vegetation of unrestored sites; and 3) similarity between seedbanks and standing vegetation. We found that few native grasses persisted in seedbanks of restored sites, with only marginally better results in terms of standing vegetation. No native grasses were found in unrestored site seedbanks and only trace amounts were detected in standing vegetation. We also found low similarity among seedbanks and between seedbanks and vegetation at all sites, suggesting a high degree of patchiness and low predictability of seedbank composition from vegetation. These results suggest that some restoration sites in the region are on undesirable trajectories, likely due to re-invasion of nonnative species. Our results further suggest that passive restoration is not a viable approach for restoring degraded sites in the region. We propose that managers incorporate seedbank analysis into monitoring efforts to more fully understand the present and future trajectories of restored and unrestored sites.
Antibiotic and metal resistance of cultivable bacteria in the Antarctic sea urchin

Abstract In this paper we report the first characterization of cultivable bacteria obtained from the Antarctic sea urchin Sterechinus neumayeri. The coelomic fluid was obtained from a pool of sea urchins which was plated onto different media to isolate the bacteria. A total of 42 isolates of psychrotrophic and aerobic γ-Proteobacteria (59.5%), Flavobacteria (33.3%) and Actinomycetes (7.2%) were isolated and sequenced. These bacteria were exposed to heavy metals and antibiotics, where 38 strains were analysed by the minimal inhibitory concentration method. Antibiotic resistance was detected in 44% of cultivable strains, and a further 13% presented co-resistance to antibiotics and heavy metals. The genera of bacteria that showed an increased resistance and co-resistance to metals and antibiotics were Flavobacterium, Psychrobacter and Pseudomonas. Additionally, 30.9% of isolated bacterial strains contained plasmids, which are probably related to resistance and co-resistance to metals. These results indicate that sea urchin-associated bacteria could be reservoirs for antibiotic resistance genes.
Analysis of a Prodigiosin Biosynthetic Gene Cluster from the Marine Bacterium Hahella chejuensis KCTC 2396

Marine bacterium Hahella chejuensis KCTC 2396 simultaneously produced red antibiotic prodigiosin and undecylprodiginine. A complete set of the prodigiosin biosynthetic gene cluster has been cloned, sequenced, and successfully expressed in a heterologous host. Sequence analysis of the gene cluster revealed 14 ORFs showing high similarity to pig and red genes from Serratia spp. and Streptomyces coelicolor A3(2), respectively, and the gene organization was almost: similar to that of pig genes. These genes were named hap for Hahella prodigiosin, and determined to be transcribed as a single operon, by RT-PCR experiment. Based on the hap gene mutagenesis experiments and comparative analysis with pig and red genes, we propose a prodigiosin-biosynthetic pathway in KCTC 2396.
The role of Quantitative variations in Connective Tissue Growth Factor gene expression in Cardiac Hypertrophy and Fibrosis

Heather E Doherty The role of Quantitative variations in Connective Tissue Growth Factor gene expression in Cardiac Hypertrophy and Fibrosis (Under the direction of Nobuyo Maeda) Connective tissue growth factor (CTGF) is a secreted, extracellular matrix (ECM) bound signaling molecule. While it stimulates maintenance and repair of the ECM, increased Ctgf gene expression is strongly associated with excess deposition of ECM in conditions of chronic organ injury and fibrotic diseases. High expression of Ctgf is also associated with cardiac fibrosis following chronic hypertension, myocardial infarction, and other cardiovascular diseases. Cardiac fibrosis is a major cause of heart dysfunction leading to heart failure, for which there is currently no effective treatments. The prevailing opinion in the field is that high expression of Ctgf causes fibrotic disease, and it has been proposed that inhibiting Ctgf expression will reduce fibrosis. This hypothesis, however, has not been directly tested. To test whether genetic variations in Ctgf expression modify hypertrophy or fibrosis, I have generated seven strains of mice that differ in their basal Ctgf expression levels across a 30-fold range, including utilizing a novel method of swapping the 3’UTR to achieve altered gene expression. Mice were naturally aged or treated with angiotensin II infusion or with transverse aortic constriction, to evaluate how altered basal Ctgf gene expression modifies cardiac hypertrophy and cardiac fibrosis related phenotypes. Contrary to the expectations, cardiac fibrosis in mice with higher basal
In Gel Detection of Lipase Activity in Crude Plant Extracts (Olea europaea)

[Abstract] Here, we provide a detailed protocol describing a SDS-PAGE based procedure to assay in gel neutral lipase activity. Total protein extracts are separated by SDS-PAGE and gels are treated with lipase substrate-α-naphthyl palmitate. This long-chain fatty acid ester is hydrolysed by lipases present in the gel. The product resulting from this reaction can be then visualized in the gel as yellowbrownish activity bands. This relatively simple and effective method of lipase assay detection can be used for crude protein extracts from different plant tissues.
of an intertidal ecosystem

The spatial structure of seagrass landscapes is typically ascribed to the direct influence of physical factors such as hydrodynamics, light, and sediment transport. We studied regularly interspaced banded patterns, formed by elongated patches of seagrass, in a small scale intertidal ecosystem. We investigated (1) whether the observed spatial patterns may arise from feedback interactions between seagrass and its abiotic environment and (2) whether changes in abiotic conditions may lead to predictable changes in these spatial patterns. Field measurements, experiments, and a spatially explicit computer model identified a "scale dependent feedback" (a mechanism for spatial self-organization) as a possible cause for the banded patterns. Increased protection from uprooting by improved anchoring with increasing seagrass density caused a local positive feedback. Sediment erosion around seagrass shoots increased with distance through the seagrass bands, hence causing a long-range negative feedback. Measurements across the depth gradient of the intertidal, together with model simulations, demonstrated that seagrass cover and mean patch size were predictably influenced by additional external stress caused by light limitation and desiccation. Thus, our study provides direct empirical evidence for a consistent response of spatial self-organized patterns to changing abiotic conditions, suggesting a potential use for self-organized spatial patterns as stress indicators in ecosystems.
Inhibition of Interleukin-1α-induced Intestinal Epithelial Tight Junction Permeability by Curcumin Treatment in Caco-2 Cells in Caco-2 Cells

The intestinal tight junction (TJ) plays an important role as a paracellular barrier. Impaired TJ permeability and enhanced proinflammatory cytokine production are crucial pathophysiological mechanisms in inflammatory bowel diseases (IBDs). Although proinflammatory cytokines, tumor necrosis factor-al-pha and interluekin-1 beta, which are markedly increased in IBD patients, have been reported to increase intestinal TJ permeability, the role of interleukin-1 alpha (IL-1 α ) in the TJ has not been studied. Phytochemicals could prevent proinflammatory cytokine-caused TJ alteration. Curcumin (CCM), a bio-logically active component of turmeric, has a strong anti-inflammatory activity. The purpose of this study was to elucidate the effect of IL-1 α on intestinal epithelial TJ permeability and the role of CCM in IL-1 α ’s action on TJ in an in vitro intestinal epithelial system, Caco-2 monolayers. The TJ integrity of Caco-2 monolayers was estimated by measuring the flux of FITC-labeled dextran and transepithelial electrical resistance (TEER). Apical IL-1 α (100 ng/ml) treatment elevated TJ permeability and sup-pressed TEER of Caco-2 monolayers. Pretreatment with CCM (20 μ M) for 30 min significantly in-hibited IL-1 α -induced TJ alterations, such as increased TJ permeability and decreased in TEER values. These results demonstrated that IL-1 α -induced increases in Caco-2 TJ permeability and CCM blocked the action of IL-1 α in the TJ. Caco-2 cells, curcumin, interleukin-1 α , intestinal epithelial tight junction, permeability
Mussel shells as an environment enrichment and calcium source for floor‐housed laying hens1

&NA; Feather pecking is still a behavioral problem in laying hen flocks, resulting in impaired welfare and economic losses. Environment enrichment, e.g., providing access to litter, to increase foraging behavior in laying hens has been shown to decrease feather pecking. This study investigated the effect of spreading crushed mussel shells (particle size 10 to 20 mm) in the litter area as an environment enrichment and source of calcium for layers receiving a commercial feed and for layers given a feed with 40% less calcium. These treatments were compared with a control involving hens given the commercial feed, but no mussel shells in the litter. The study included 900 Dekalb White layers housed in a single‐tier floor system during a production cycle (20 to 72 wk of age). The mussel shells were consumed to a lower extent than predicted, resulting in calcium deficiency in hens fed the low‐calcium diet. This in turn was evident as increased degree of keel bone deviations and lower eggshell breaking strength. Daily addition of crushed mussel shells to the litter for laying hens on a balanced or calcium‐deficient diets did not generate any positive effects on bird feather cover, eggshell quality, production performance, or fearfulness. Hence, with the particle size of mussel shells used in this study, there was no indication of improved welfare due to environment enrichment.
High phosphorus supply increases persistence and growth of white clover in grazed dairy pastures during dry summer conditions

Measurements of pasture appearance, white clover leaf and stolon mass, stolon water potential, and percentage clover cover in the sward were made for grazed dairy pastures at Ellinbank, West Gippsland, Victoria, during the hot, dry month of February 1997. The perennial ryegrass–white clover-based pastures were in rotationally grazed paddocks from a large farmlet experiment and had received different levels of phosphorus fertiliser (0 or 280 kg P/ha over an 18-month period), and were being grazed with 2 or 3 cows/ha for the no-phosphorus, or 3 or 4 cows for the high-phosphorus paddocks. Further measurements of white clover composition in the pasture swards were made in April, following autumn rain. There were marked differences in white clover (i.e. more yellow, flaccid and desiccated plants with fewer leaves) and pasture appearance (higher frequency of patchy, weedy, poorly utilised areas) in the no-phosphorus, compared with the high-phosphorus treated pastures with the same stocking rate of 3 cows/ha. Also, the high-phosphorus paddocks had a greater white clover percentage than the low-phosphorus paddocks in February with mean percentages of 13.8 and 7.8% respectively. Following rains in March and April, the mean percentage clover cover in high-phosphorus paddocks had increased substantially by 30 April 1997 to 30.6% whereas there was a small improvement in mean clover content in the low-phosphorus paddocks (12.3%). The white clover plants in the high-phosphorus paddocks had heavier stolons, larger leaves and, for the medium stocking rate (3 cows/ha), they appeared to have more leaves per cm of stolon. The findings support previous studies which have highlighted how high-phosphorus application rates can improve the performance of repeatedly defoliated white clover plants during dry periods.
Model Studies Characterizing the Rheological Behavior of Simulated Mashing Conditions Using the Rapid Visco-Analyzer

This paper reports on the application of the rapid visco-analyzer (RVA) to further understand rheological changes that are taking place during the brewery mashing process. Clear correlations were found between the level of amylase present in mashes and the rheological data points representing primary grain/starch swelling and subsequent starch digestibility. In addition, secondary starch gelatinization rheological data representing consistency-viscosity increases because of the presence of smaller starch granules were clearly correlated with the level of mash amylase. The influence of mash pH on starch gelatinization/liquefaction and amylase activities could be quantified from the rheological data. Clear correlations were found between the added levels of β-glucanase on a β-glucan substrate and the recorded rheological trends. Overall, the studies clearly show the interactions between grain components (purified/nonpurified), amylolytic enzymes, glucanolytic enzymes, and mash pH and how they individually and collectively influence the consistency-viscosity profiles during the mashing process. In addition, the results further validate the RVA as being a suitable instrument for determining mash rheological changes. Application of the methods can provide the maltster, brewer, or distiller with more functional information regarding raw materials and process conditions.
Zur Herpetofauna des Beckens von Köyceğiz, Türkei (Dalyan-Region)

3 species of amphibians and 21 species of reptiles have been found in the basin of Koycegiz in southwest Anatolia. The species are listed with short descriptions of their occurrence. The rich herpetofauna emphasizes the need for a striCt protection of the whole basin. The need for the conservation of regional herpetofaunas in Turkey is discussed.
Cigarette smoke‐induced pro‐inflammatory alterations in the endothelial phenotype: role of NAD(P)H oxidase activation

Although the cardiovascular morbidity and mortality induced by cigarette smoking exceeds that attributable to lung cancer, the molecular basis of smoking‐induced vascular injury remains unclear. To test the link between cigarette smoke, oxidative stress and vascular inflammation, rats were exposed to the smoke of 5 cigarettes per day (for one week). Also, isolated arteries were exposed to cigarette smoke extract (CSE; 0 to 40 ug/mL, for 6 h) in organoid culture. We found that smoking impaired acetylcholine‐induced relaxations of carotid arteries, which could be improved by the NAD(P)H oxidase inhibitor apocynin. Both smoking and in vitro CSE exposure significantly increased vascular O2. ‐ and H2O2 production. Vascular mRNA expression of the pro‐inflammatory cytokines IL‐1beta, IL‐6 and TNFalfa and that of iNOS was significantly increased by both smoking and CSE exposure, which could be prevented by inhibition of NAD(P)H oxidase (DPI, apocynin) or scavenging of H2O2. In cultured endothelial cells CSE elicited NF‐kB activation and increased monocyte adhesiveness, which were prevented by apocynin and catalase. Thus, we propose that water soluble components of cigarette smoke (that are likely to be present in the bloodstream in vivo in smokers) activate the vascular NAD(P)H oxidase. NAD(P)H oxidase‐derived H2O2 activates NF‐kB leading to pro‐inflammatory alterations in vascular phenotype, which likely promotes development of atherosclerosis, especially if other risk factors are also present.
Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within a local area or even a few hundred square meters. Understanding ecological patterns and how plants respond to global warming and human alteration of landscapes and ecosystems necessitates a holistic approach. Such an approach must be conducted at a scale that is commensurate with the breadth of the questions being asked. Further, it requires identification, retrieval, and integration of diverse data from a global confederation of collaborating scientists across a broad range of disciplines. We propose to network core databases and data networks to create a novel resource for quantitative plant biodiversity science. The grand challenge is to assemble and share the world’s rapidly accumulating botanical information from plots and collections to create a distributed, web-accessible, readily analyzable data resource. With such a resource, we will answer major questions of direct relevance to plant ecology, plant evolution, plant geography, conservation, global change biology, and protection of biodiversity and ecosystem services. In particular, how does climate influence the distribution and abundance of plant species, how does the phylogenetic diversity of plants vary across broad environmental and climatic gradients, and how are plants assembled into ecological communities? While these and associated questions are at the core of many research endeavors in comparative botany and ecology, our past collective inability to integrate data on a large scale has significantly limited our ability to address these questions head on. This proposed Grand Challenge team will create a data resource of unprecedented size and scope together with the tools for its use, thereby empowering botanists and the general public to better address fundamental issues in plant ecology and global change biology. Although we will focus on plants of the New World, the infrastructure and protocols developed will be scalable to all geographic regions and all types of organisms. Future steps will enable cross-cutting linkages to emerging networks on plant genomics, physiology, and phylogeny, allowing us to address fundamental genetic and evolutionary questions at unprecedented spatial and temporal scales.
Characterization of the metK and yitJ leader RNAs from the Bacillus subtilis S Box regulon

ii DEDICATION . v ACKNOWLEDGEMENTS . vi VITA . viii LIST OF TABLES . xv LIST OF FIGURES . xvi LIST OF ABBREVIATIONS . xx CHAPTER 1 . 1 REGULATION OF GENE EXPRESSION BY RIBOSWITCHES . 1 1.1 Types of riboswitch classes . 7 1.2 Riboswitch classes . 10 1.2. 1 RNA Thermosensors . 10 1.2. 2 T box riboswitch . 15 1.2. 3 Amino acid binding riboswitches . 19 1.2. 3.1 L box riboswitch . 19 1.2. 3.2 Glycine riboswitch . 21 1.2. 3.3 Glutamine riboswitch . 24 1.2. 4 Purine-sensing riboswitches. 26
Intranasal Low-Dose Naltrexone Against Opioid Side Effects: A Preclinical Study

Opioids are broad spectrum analgesics that are an integral part of the therapeutic armamentarium to combat pain in the clinical practice. Unfortunately, together with analgesia, a number of adverse effects can occur such as nausea, vomiting, constipation, gastrointestinal alterations and cognitive impairments. Naltrexone is a competitive antagonist of opioid receptors commonly used to treat opioid addiction; its oral use against agonists side effects is limited by the decrease of opioids-therapeutic efficacy and own adverse effects. The intranasal delivery of naltrexone could offer a quick and effective achievement of CNS based on extracellular mechanisms including perineural and perivascular transport. The aim of the study was to test the efficacy of intranasal low-dose naltrexone in reducing intraperitoneal morphine and oxycodone side effects in rodents. In mice, 1 μg naltrexone intranasally administered 30 min before opioids reduced cognitive impairments and motor alteration induced by 10 mg kg−1 morphine and 60 mg kg−1 oxycodone in the Passive avoidance and Rota rod tests, respectively. Moreover, naltrexone rebalanced opioid-induced reduction of the intestinal transit and latency of feces expulsion as well as food intake inhibition. Importantly, 1 μg naltrexone instillation did not block analgesia as demonstrated by the Hot plate test. In rats, intranasal naltrexone counteracted the opioid-induced pica phenomenon related to emesis and increased water and palatable food intake. The effects were comparable to that achieved by metoclopramide used as reference drug. Treatments did not influence body weight. Lastly, the safety of the intranasal delivery has been checked by hematoxylin–eosin staining that did not show histological alterations of the nasal cavity. In conclusion, intranasal low-dose naltrexone counteracted morphine and oxycodone induced gastrointestinal and CNS side effects without impairing opioid analgesia. It is a candidate to be a valid clinical strategy deserving deep analysis.
Molecular characterisation of the pro-apoptotic molecules APAF1 and Smac

Molecular Characterisation of the Pro-Apoptotic Molecules APAF1 and Smac by Darren Leslie Roberts. Apoptosis is a key process involved in cell number regulation and a range of pathological disorders. It is a highly structured process that removes the cell from the body without damage to surrounding cells. The mitochondria has been shown to play a key role in apoptosis induced by a wide range of stimuli and can trigger the apoptotic pathway by release of apoptogenic factors. One of these factors is cytochrome c, a protein that normally functions in the electron transport chain but upon release it binds to the first mammalian homologue of CED-4, Apoptotic Protease Activating Factor 1 (APAF1) and induces the formation of a large caspase-activating complex. Another protein released from the mitochondria is Smac, a pro-apoptotic protein that functions by antagonising Inhibitor of Apoptosis Protein function. The data presented in this thesis demonstrated the existence of multiple splice forms of both APAF1 and Smac and investigated their roles in the apoptotic pathway. APAF1 forms the large molecular weight complex known as the apoptosome in 293 cells although epitope tagged APAF1 formed an incorrectly formed this complex in the absence of additional stimuli. APAF1 was also found to be cleaved by Caspase-3 during apoptosis and that the resulting 30 kDa fragment is associated with the inactive complex. Data also indicates that caspase-9 recruitment to the apoptosome occurs via interactions between both the CARD and the CED-4 homologous regions of APAF1. The pro-apoptotic protein Smac exists as several forms due to alternative splicing and one of these forms, Smac p, is pro-apoptotic even though it lacks the N-terminal Inhibitor of Apoptosis protein binding domain. Smac p is localised to the cell cortex and does not redistribute upon induction of apoptosis. These data demonstrate that Smac is able to induce apoptosis independently of Inhibitor of Apoptosis Protein binding. A polyclonal antibody to Smac / Smac p was also developed and characterised.