Miracle-dz/UniFAR-FTUs huggingface dataset:
Climate change and plant regeneration from seed

At the core of plant regeneration, temperature and water supply are critical drivers for seed dormancy (initiation, break) and germination. Hence, global climate change is altering these environmental cues and will preclude, delay, or enhance regeneration from seeds, as already documented in some cases. Along with compromised seedling emergence and vigour, shifts in germination phenology will influence population dynamics, and thus, species composition and diversity of communities. Altered seed maturation (including consequences for dispersal) and seed mass will have ramifications on life history traits of plants. Predicted changes in temperature and precipitation, and thus in soil moisture, will affect many components of seed persistence in soil, e.g. seed longevity, dormancy release and germination, and soil pathogen activity. More/less equitable climate will alter geographic distribution for species, but restricted migratory capacity in some will greatly limit their response. Seed traits for weedy species could evolve relatively quickly to keep pace with climate change enhancing their negative environmental and economic impact. Thus, increased research in understudied ecosystems, on key issues related to seed ecology, and on evolution of seed traits in nonweedy species is needed to more fully comprehend and plan for plant responses to global warming.
Using an Agroecological Approach to Farming Systems Research

Iowa State University journal series 19573. We gratefully acknowledge the help of the following individuals who assisted with this research or reviewed this manuscript: C. Cambardella, M. Duffy, D. Karlen, B. Burcham, R. Turnbull, and H. Friedrich. We also thank the Leopold Center for Sustainable Agriculture and the USDA–IFAFS (Initiative for Future Agriculture and Food Systems) program for funding this project, and Iowa State University College of Agriculture, the Neely-Kinyon Association, and Heartland Organic Marketing Cooperative for their support of this research and education program. ADDITIONAL INDEX WORDS. farming systems research, organic, compost, soil quality, long-term research
Diversity among Grapevine Leafroll-associated Virus 2 Isolates Detected by Heteroduplex Mobility Assay

Grapevine leafroll-associated virus 2 (GLRaV-2) was detected by serological and molecular analyses in several grapevine accessions of different varieties from Italian, Greek, French and Brazilian vineyards in a 2001-2002 survey. In order to study the genetic variability among GLRaV-2 isolates in the open reading frame (ORF) coding the coat protein (CP), heteroduplex mobility assays were performed on 17 isolates and six strains used as reference. Eight diverse GLRaV-2 variants were identified among the infected grapevines tested. The most common variant was found in the majority of the samples characterized; it was indistinguishable from the reference strains from the Semillon and Pinot noir 95 accessions. GLRaV-2 variants found in Italian cvs Negro amaro and Vermentino were identical to the reference strain from cv. Muscat de Samos (Greece). Three other GLRaV-2 variants from Southern and Central Italy were different from all the reference strains. A grapevine accession from Tuscany was found to contain two diverse GLRaV-2 variants. None of the variants tested sample identical to the American strain H4 or the reference strains from cvs Chasselas 8386 (Switzerland) or Alphonse Lavallee 224 (France); the latter three accessions were different from one another. The estimated nucleotide homology in CP gene among 23 GLRaV-2 isolates was in some cases < 88%.
Polyandry in the mind bug Lygocoris pabulinus (L.)—effects on sexual communication and fecundity

Summary Lygocoris pabulinus females are polyandrous under laboratory conditions (Groot et al., 1998). As the insect mating system affects sexual communication and thus sexual behavior as a whole, we studied sperm transfer, storage and displacement in L. pabulinus. To be able to fully understand these processes, detailed information on the female reproductive tract is essential. Therefore, we first studied the female genitalia in detail. The bursa copulatrix consists of four plates, and a spermatheca is connected anteriorly to the bursa. At copulation a spermatophore is formed in the spermatheca. The spermatophore is compartmentalized, consisting of a sperm-containing portion, a large sperm-free portion and a mating plug. After 24 h the spermatophore has partially disintegrated. The mating plug is still intact but reduced in size. Sperm are found throughout the spermatheca and in the median and lateral oviducts where fertilization most likely takes place. The amount of male-derived substances transferred to females during first matings was ca. 5.2% relative to male body weight. To understand the effects of matings on the sexual communication, we determined sexual attraction of mated females at long and close range. At long range females were unattractive for only 1–2 h after mating, while they remained attractive at close range. Mated males were not attracted to virgin females for 2 h after mating, and only 23% of the tested males mated again within 24h. Together, these results suggested a high paternal investment that may affect reproductive output. To determine if this is the case, and hence if multiple matings affect fecundity and/or longevity, we conducted two oviposition experiments. From these experiments no positive effects on total fecundity or longevity in multiply mated females were apparent.
Mollusc communities of lowland rivers and oxbow lakes in agricultural areas with anthropogenically elevated nutrient concentration

Anthropogenically elevated nutrient concentration occurs in both ground and surface waters and cause grave environmental problems which are responsible for the degradation of water quality on a worldwide scale. The progressive anthropogenic pressure caused by prolonged agricultural activity has a negative effect on most water ecosystems including rivers and reservoirs. Freshwater molluscs, which are hololimnic organisms, have a limited mobility; therefore, they are good bioindicators of changes in their habitats. They reflect the abiotic or biotic state of water habitats, which represents the impact of environmental change on the habitat, community as well as on the ecosystem. A long-term survey of mollusc communities revealed the occurrence of 44 species including some rare, vulnerable, threatened or legally protected species, e.g. Borysthenia naticina, Unio crassus, Anodonta cygnea, Pseudanodonta complanata or Sphaerium rivicola, in the Wkra River, its tributaries and selected oxbow lakes. In the Wkra River catchment area, the mollusc communities, including U. crassus (Habitats Directive Natura 2000), are under a combined effect of several environmental factors. Conductivity, hardness, current velocity, river width, temperature, nutrient concentration and the size of sediment particles were the parameters most associated (statistically significant according to the forward selection results) with the distribution of mollusc species. The forward selection results showed that the concentration of dissolved oxygen and the occurrence of macrophytes also exerted a significant influence on the distribution of Mollusca. Among environmental factors, anthropogenically elevated concentrations of nitrites and nitrates in the water were the most predictive parameters that negatively influenced (stressors) the structure of mollusc communities. The novel findings of this survey showed that some mollusc species could tolerate wider ranges of some environmental factors and higher concentrations of nutrients than had been expected. U. crassus is more tolerant of a relatively high concentration of nitrates in the water than was previously expected, as well as of nitrites and phosphates, and it can survive in rivers with relatively high nutrient concentration. The present results confirm both the field and the toxicological research on the negative effect of nitrites and nitrates, which is caused by their toxicity to freshwater molluscs. The number of individuals, number of mollusc species and density decreased dramatically within the last year of the survey in the Wkra River and its tributaries. This phenomenon seems to be a direct result of the nutrient enrichment in the Wkra River catchment area, the regulation of riverbeds or an indirect result, e.g. lack of primary or appropriate host fishes for unionid species. The declining trend in the global mollusc population has probably begun to occur in the Wkra River catchment area.
In vitro synthetic transcriptional networks

Information processing using biochemical circuits is essential for survival and reproduction of natural organisms. Construction of synthetic biochemical circuits from simple components provides a useful approach to establish the minimal determinants required for complex logical functions. As stripped-down analogues of genetic regulatory networks in cells, we engineered artificial transcriptional networks consisting of synthetic DNA switches, regulated by RNA signals acting as transcription activators or repressors, and two enzymes, bacteriophage T7 RNA polymerase and Escherichia coli ribonuclease H. The synthetic switch design is modular with programmable connectivity and allows dynamic control of RNA signals through enzyme-mediated production and degradation. The switches support sharp and adjustable thresholds using a competitive hybridization mechanism, analogous to a biological threshold mechanism, "inhibitor ultrasensitivity," thus allowing arbitrary analog or digital circuits to be created in principle. Theoretical correspondence of our biochemical network to neural networks where synaptic weights and thresholds are encoded by concentrations of DNA strands greatly facilitates network design and analysis. Experimentally, we have constructed and analyzed several simple networks: positive and negative autoregulatory circuits, a mutual inhibitory circuit, and oscillators with positive and negative feedback. Reasonable agreement between experimental data and a simple mathematical model was obtained for switch input/output functions, phaseplane trajectories, the bifurcation diagram, and oscillation periods. A systematic quantitative characterization lead to identification of important network properties such as the saturation of degradation machinery and challenges to understand such as the interference by incomplete RNA signals. Construction of larger synthetic circuits provides a unique opportunity for evaluating model inference, prediction, and design of complex biochemical systems and could be used to ontrol nanoscale devices and artificial cells.
IFN-γ, IFN-β, and PGE Affect Monokine Secretion: Relevance to Monocyte Activation in Multiple Sclerosis

Abstract Activated antigen-presenting cells and central nervous system microglia produce IL-1β, TNF-α, IL-6, and PGE1. These monokines participate in the lymphocyte activation, demyelination, and intrathecal immunoglobulin synthesis seen in multiple sclerosis (MS). Exacerbations of MS are ameliorated by IFN-β, but provoked by IFN-γ, possibly through an effect on monocytes (Mo). We studied the effects of IFNs and PG on monokine secretion under stringent low-endotoxin conditions. Spontaneous and IFN-γ-induced IL-1β secretion was greater in MS than in NL Mo. IFN-β did not inhibit IFN-γ-induced secretion of monokines, which contrasts with IFN-β's inhibitory effect on IFN-γ-induced MHC class II expression. PGEt, a cAMP agonist, caused a 30-fold induction of IL-6 secretion. Indomethacin directly inhibited this induction. Low-close IFN-β, through effects on T cells, and cAMP agonists, through effects in T cells and Mo, may ameliorate inflammatory diseases characterized by excessive monokine secretion.
Reproductive Genetics and Epigenetics of F1 hybrid triploids of Arabidopsis thaliana L.

XII CHAPTER 1 – GENERAL INTRODUCTION . 1 1. Arabidopsis thaliana a model species in plant biology and beyond . 2 1.1 The first sequenced plant species . 2 1.2 Identification of Arabidopsis thaliana gene function – analysis of mutants . 3 1.3 Natural genetic variation among Arabidopsis thaliana accessions . 4 1.4 Polymorphism (SNPs) discovery among Arabidopsis thaliana natural accessions . 6 1.5 Mapping large-effect loci from qualitative variation . 7 1.6 Mapping loci from quantitative variation . 8 1.7 Genome-wide association (GWA) mapping potentials and pitfalls . 9 2. Arabidopsis thaliana sexual reproduction and seed development . 12 2.1 Plant life cycle . 12 2.2 Flowering time . 12 2.3 Gametogenesis . 13 2.4 Double fertilization . 14 2.5 Seed development . 15 3. Seed size control . 16 3.1 Parental effects . 17 3.2 Parent-of-origin dosage effects . 20 3.3 Epigenetic regulation of endosperm development . 20 4. Whole genome changes and their implications for plant reproduction . 26 4.1 Polyploidy . 26 4.2 Aneuploidy . 29 4.3 Hybridization . 31 4.4 Heterosis . 34 4.5 Apomixis. 37 5. Summary . 39
Broad tumor-associated expression and recognition by tumor-derived γδ T cells of MICA and MICB

Human MHC class I-related molecules, MICA and MICB, are stress-induced antigens that are recognized by a subset of γδ T cells expressing the variable region Vδ1. This functional association has been found to be limited to intestinal epithelium, where these T cells are prevalent and where MICA and, presumably, MICB are mainly expressed. However, increased frequencies of Vδ1 γδ T cells have been observed in various epithelial tumors; moreover, MICA/B are expressed on diverse cultured epithelial tumor cells. With freshly isolated tumor specimens, expression of MICA/B was documented in many, but not all, carcinomas of the lung, breast, kidney, ovary, prostate, and colon. In tumors that were positive for MICA/B, the frequencies of Vδ1 γδ T cells were significantly higher than in those that were negative. Vδ1 γδ T cell lines and clones derived from different tumors recognized MICA/B on autologous and heterologous tumor cells. In accord with previous evidence, no constraints were observed in these interactions, such as those imposed by specific peptide ligands. Thus, MICA/B are tumor-associated antigens that can be recognized, in an apparently unconditional manner, by a subset of tumor-infiltrating γδ T cells. These results raise the possibility that an induced expression of MICA/B, by conditions that may be related to tumor homeostasis and growth, could play a role in immune responses against tumors.
ANTIBACTERIAL ACTIVITIES OF HONEY, SANDAL OIL AND BLACK PEPPER

The purpose of the present study was to determine the antibacterial activities of honey, sandal oil and black pepper by taking a selected standard medicine. These products are used for the treatment of various diseases. The bacterial isolates obtained from clinical samples were Escherichia coli, Salmonella sp. , Staphylococcus aureus and Bacillus subtilis. After identification and confirmation the pure culture of clinical bacterial isolates were used to test the sensitivity of bacterial isolates against sample products. Dimethyl sulfoxide and distilled water were used as solvent for sample products. Different types of honey, sandal oil and black pepper were tested against bacterial isolates. Results of all sample products showed zone of inhibition against all selected bacterial isolates. At the dilution of 25µl of stock solution in 75µl and at 50µl: 50µl concentration, the results were similar as obtained from honey and sandal oil. Dimethyl sulfoaxide DMSO and honey 1 showed inhibition zones against all except Staphylococcus aureus, whereas honey 2 was effective against all isolates. Sandal 1 oil showed inhibition zones against all isolates except E.coli whereas sandal 2 was effective against all. The results obtained from black pepper 1 and 2 did not gave effective results both at 50µ litre: 50µ litre and 25µ litre: 75µ litre concentration, both were found to be effective against Bacillus subtilus. Standard medicine showed inhibition zone against all selected bacterial isolates in each test.
Curcumin (Diferuloylmethane) Inhibits Receptor Activator of NF-κB Ligand-Induced NF-κB Activation in Osteoclast Precursors and Suppresses Osteoclastogenesis1

Numerous studies have indicated that inflammatory cytokines play a major role in osteoclastogenesis, leading to the bone resorption that is frequently associated with cancers and other diseases. Gene deletion studies have shown that receptor activator of NF-κB ligand (RANKL) is one of the critical mediators of osteoclastogenesis. How RANKL mediates osteoclastogenesis is not fully understood, but an agent that suppresses RANKL signaling has potential to inhibit osteoclastogenesis. In this report, we examine the ability of curcumin (diferuloylmethane), a pigment derived from turmeric, to suppress RANKL signaling and osteoclastogenesis in RAW 264.7 cells, a murine monocytic cell line. Treatment of these cells with RANKL activated NF-κB, and preexposure of the cells to curcumin completely suppressed RANKL-induced NF-κB activation. Curcumin inhibited the pathway leading from activation of IκBα kinase and IκBα phosphorylation to IκBα degradation. RANKL induced osteoclastogenesis in these monocytic cells, and curcumin inhibited both RANKL- and TNF-induced osteoclastogenesis and pit formation. Curcumin suppressed osteoclastogenesis maximally when added together with RANKL and minimally when it was added 2 days after RANKL. Whether curcumin inhibits RANKL-induced osteoclastogenesis through suppression of NF-κB was also confirmed independently, as RANKL failed to activate NF-κB in cells stably transfected with a dominant-negative form of IκBα and concurrently failed to induce osteoclastogenesis. Thus overall these results indicate that RANKL induces osteoclastogenesis through the activation of NF-κB, and treatment with curcumin inhibits both the NF-κB activation and osteoclastogenesis induced by RANKL.
ANTIRETROVIRAL TOXICITY AND OXIDATIVE STRESS

Antiretroviral drugs are used for the treatment of human immunodeficiency virus, they are used as combination regimens to achieve the highest possibl e benefit, tolerability, compliance and to diminish the risk of resistance development. Reports from precli nical and clinical studies have linked antiretrovir als with some toxicological effects which could be associate d with redox imbalance (oxidative stress). This stimulated us to review relevant literature on the relationship between antiretroviral induced toxicol ogical effects and redox imbalance. Available literature o n antiretroviral associated toxicological effects a nd oxidative stress were comprehensively reviewed. Lit erature showed that antiretrovirals are associated with toxicological effects which includes hepatotox icity, cardiotoxicity, hematotoxicity and nephrotoxicity. Reports in animal studies also show ed that these toxicological effects could be associated with oxidative stress through the genera tion of oxidative radicals, depletion of antioxidan ts and antioxidant enzymes leading to mitochondria damage in the heart, kidney, liver brain and other organs. In humans, studies also showed that antiret rovirals are associated with lipid peroxidation, depletion of antoxidants and antioxidant enzymes wh ich are elements of oxidative stress. Furthermore it was observed that supplementations with some ant ioxidants mitigated antiretroviral induced oxidative stress, mitochondria damage and toxicolog ical effects. Antiretroviral drugs are associated with toxicological effects which may involve redox imbalance, but more studies are required to correlate antiretroviral toxicities with oxidative stress.
Structural changes of the testis and changes in semen quality parameters caused by intraperitoneal and peroral administration of selenium in rats.

The aim of this study was to find the structural changes in the testis and semen quality parameters of rat after a singleintraperitoneal and repeated peroral selenium administration. Rats were killed 36 hours following the intraperitonealadministration of selenium selenite (2 mg.kg-1 b.w.; 98% purity) and after 90 days of the peroral repeatedadministration of selenium in drinking water (5 mg.l-1). Testis samples were evaluated by histological andmorphometrical methods in light microscopy. Evaluation of semen samples were examined with CASA method. 36hours after the selenium i.p. administration, damage of cellular associations, release of necrotised epithelial cells totubule lumen and fibrotisation and extension of interstitium were observed. Morphometry methods have shown thereduction of seminiferous epithelium volume (P<0.001), extension of interstitium (P<0.001) and increased area ofintraepithelial spaces (P<0.01). In p.o. group similar but more intense changes were noted; in addition, occasionalldegeneration of seminiferous tubuli and rarely total damage in histoarchitecture of seminiferous epithelium wereobserved. CASA analysis revealed significant decrease in all parameters except the concentration of spermatozoa.Additionally, we suppose that p.o. dose 5 mg.l-1 sodium selenite in drinking water is minimum lethal dose level foryoung rats. Selenium after i.p. and p.o. administration causes damage of seminiferous epithelium and interstitium. Itleads to changes in relative proportion of functional tissues of the testis. Reduced spermatogenesis and harmfuleffects in semen parameters are characteristic especially for peroral repeated (subchronic) administration. Thesechanges are time- and dose-dependent. In both dosage methods subfertility or infertility can appear.
Distributions of planktonic sea lice larvae Lepeophtheirus salmonis in the inter-tidal zone in Loch Torridon, Western Scotland in relation to salmon farm production cycles

This study examines the relative density of sea lice, Lepeophtheirus salmonis (Kroyer), larvae in the inter-tidal areas of Loch Torridon, a fjordic sea loch in Western Scotland and the site of several commercial salmon farms. Samples of planktonic sea lice were collected in each spring from 1999 to 2003 near the mouth of the River Shieldaig, where sea trout have been shown to congregate in the first few days after going to sea, and from 2001 to 2003 near the mouth of the River Balgy. No larval sea lice were found near the mouth of the River Shieldaig in spring 2000 or 2002, when gravid female sea lice were absent on local fish farms. The same finding was observed in 2002 at the mouth of the River Balgy. In springs of 1999, 2001 and 2003, peak densities of larval sea lice of 33, 94 and 143 m−3, respectively, were observed at the mouth of the river Shieldaig. At the mouth of the River Balgy, peak densities of 74 and 78 lice m−3 were observed in 2001 and 2003 respectively. At the time these samples were collected, the two local salmon farms were in the second year of their production cycle and gravid female sea lice were present. Samples of larval sea lice were also obtained year round, at approximately weekly intervals, from a 50-m transect at the mouth of the River Shieldaig, from March 2001 to June 2003, and compared with frequencies of gravid female sea lice on the two local salmon farms. High levels were found in the winter. No planktonic sea lice were found in this transect when gravid females were not present on the local fish farms.