Miracle-dz/UniFAR-FTUs huggingface dataset:
Essential Role of NF-κB-Inducing Kinase in T Cell Activation Through the TCR/CD3 Pathway1

NF-κB-inducing kinase (NIK) is involved in lymphoid organogenesis in mice through lymphotoxin-β receptor signaling. To clarify the roles of NIK in T cell activation through TCR/CD3 and costimulation pathways, we have studied the function of T cells from aly mice, a strain with mutant NIK. NIK mutant T cells showed impaired proliferation and IL-2 production in response to anti-CD3 stimulation, and these effects were caused by impaired NF-κB activity in both mature and immature T cells; the impaired NF-κB activity in mature T cells was also associated with the failure of maintenance of activated NF-κB. In contrast, responses to costimulatory signals were largely retained in aly mice, suggesting that NIK is not uniquely coupled to the costimulatory pathways. When NIK mutant T cells were stimulated in the presence of a protein kinase C (PKC) inhibitor, proliferative responses were abrogated more severely than in control mice, suggesting that both NIK and PKC control T cell activation in a cooperative manner. We also demonstrated that NIK and PKC are involved in distinct NF-κB activation pathways downstream of TCR/CD3. These results suggest critical roles for NIK in setting the threshold for T cell activation, and partly account for the immunodeficiency in aly mice.
Communities of soil macrofauna in green spaces of an urbanizing city at east China

Evaluamos la diversidad de las comunidades de macrofauna del suelo que habitan los espacios verdes urbanos en la ciudad de Yancheng, una ciudad en proceso de urbanizacion situada al este de China. A fines de abril 2011, la riqueza taxonomica, abundancia y composicion de comunidades de macrofauna del suelo fueron evaluadas y comparadas entre cinco tipos de espacio verde (bosque de alamos, granja de colza, pastizal de parque, cesped y jardin vivero) y tres capas de profundidad del suelo, con resolucion taxonomica a nivel de orden. La riqueza taxonomica (de ordenes) y la abundancia fueron significativamente diferentes entre los espacios verdes. Los indices de diversidad (riqueza taxonomica R de Margalef y diversidad H' de Shannon-Weaver) fueron mayores en el bosque de alamos, pastizal de parque y jardin vivero que en la granja de la colza y el cesped. La riqueza taxonomica (Chao 2) mostro una tendencia similar. Hubo efectos significativos del tipo de espacio verde y capa del suelo, los cuales mostraron una interaccion significativa afectando la composicion de la macrofauna. Recomendamos que los espacios verdes urbanos se puedan utilizar para mantener la biodiversidad, y no solo con propositos de paisaje.
Effect of Methotrexate and Tea Polyphenols on the Viability and Oxidative Stress in MDA-MB-231 Breast Cancer Cells

Aim: To determine the effect of tea polyphenols and methotrexate on viability and reactive oxygen species (ROS) in a naturally resistant breast cancer cell line MDA-MB-231.Methodology: MDA-MB-231 cells were selected as a model for methotrexate resistant breast cancer. Drug tests were performed over 72 hours at concentrations 0-100 µM. Pre-treatments were with quercetin (QE) or epigallocatechin gallate (EGCG) for 5 hours followed by methotrexate. Cytotoxicity was measured using the MTT assay or resazurin fluorescence assay. ROS was determined using the 2’, 7’-dichlorofluorescein diacetate assay. Intracellular GSH was measured using the monochlorobimane assay.Results: Methotrexate was cytotoxic to MDA-MB-231 cells with IC50 of 35±4 µM. The IC50 value was 68±9.4 µM with QE and 83±16 µM for EGCG. The pre-treatment with QE and EGCG lowered the IC50 for methotrexate by 28% (P =0.009) and 16% (P=0.2027). Intracellular ROS concentrations increased after treatment with methotrexate, QE or EGCG singly and ROS decreased with combination treatment compared with the response for methotrexate only. There were no significant changes in intracellular GSH. Conclusion: Pretreatment with tea polyphenols partially sensitized breast cancer cells towards methotrexate and decreases intracellular ROS. More research is needed to optimize the sensitizing effect of tea phenols on the breast cancer cell response to methotrexate.
Resistance to Tumor Necrosis Factor-α (TNF-α)-induced Apoptosis in Rat Hepatoma Cells Expressing TNF-α Is Linked to Low Antioxidant Enzyme Expression*

In order to study the mechanisms of resistance to tumor necrosis factor-α (TNF-α), we have constructed two stable transfectants producing TNF-α (Yv12–2 and Yv13–44) from the rat hepatoma H4IIE cell, which does not produce TNF-α. H4IIE cells were highly sensitive to apoptosis induced by TNF-α, whereas Yv2–12 and Yv13–44 cells were resistant. Manganous superoxide dismutase was not up-regulated in Yv2–12 and Yv13–44 cells and was unresponsive to induction by exogenous TNF-α and by H2O2 in H4IIE cells and in the transfectants. Catalase expression and activity were lower in Yv2–12 and Yv13–44 cells than in H4IIE cells; furthermore, the transfectants were more susceptible to H2O2. Treatment with exogenous TNF-α down-regulated catalase in H4IIE cells but not in Yv2–12 and Yv13–44 cells. Treatment of H4IIE cells with the catalase inhibitor 3-amino-1,2,4-triazole rendered them resistant to exogenous TNF-α. These data suggest a causal relationship between resistance to TNF-α and low catalase activity. Expression of copper and zinc containing superoxide dismutase was also decreased, whereas expression of glutathione peroxidase-1 was unchanged in Yv2–12 and Yv13–44 cells. Data from a microarray point to a down-regulation of genes in the resistant clones that code for antioxidative proteins and proteins involved in glutathione synthesis and function. We assume that a prooxidant signal linked to the down-regulation of antioxidant defense may be associated with resistance to apoptosis induced by TNF-α.
Endothelium-Mimicking Multifunctional Coating Modified Cardiovascular Stents via a Stepwise Metal-Catechol-(Amine) Surface Engineering Strategy

Stenting is currently the major therapeutic treatment for cardiovascular diseases. However, the nonbiogenic metal stents are inclined to trigger a cascade of cellular and molecular events including inflammatory response, thrombogenic reactions, smooth muscle cell hyperproliferation accompanied by the delayed arterial healing, and poor reendothelialization, thus leading to restenosis along with late stent thrombosis. To address prevalence critical problems, we present an endothelium-mimicking coating capable of rapid regeneration of a competently functioning new endothelial layer on stents through a stepwise metal (copper)-catechol-(amine) (MCA) surface chemistry strategy, leading to combinatorial endothelium-like functions with glutathione peroxidase-like catalytic activity and surface heparinization. Apart from the stable nitric oxide (NO) generating rate at the physiological level (2.2 × 10−10 mol/cm2/min lasting for 60 days), this proposed strategy could also generate abundant amine groups for allowing a high heparin conjugation efficacy up to ∼1 μg/cm2, which is considerably higher than most of the conventional heparinized surfaces. The resultant coating could create an ideal microenvironment for bringing in enhanced anti-thrombogenicity, anti-inflammation, anti-proliferation of smooth muscle cells, re-endothelialization by regulating relevant gene expressions, hence preventing restenosis in vivo. We envision that the stepwise MCA coating strategy would facilitate the surface endothelium-mimicking engineering of vascular stents and be therefore helpful in the clinic to reduce complications associated with stenosis.
Electroporation of a Foreign Gene into Black Porgy Acanthopagrus schlegeli Embryos.

growth hormone cDNA (opAFPGHc) into fertilized black porgy eggs via electroporation. One hundred fertilized eggs were collected in a 1 ml cuvette and resuspended in 100ƒÊl sterilized artificial seawater. After examining 90 different combinations of electroporation amplitude, pulse number and cycles at a constant pulse time of 160ƒÊs, burst time 0.4s and electrode distance 1 mm, we found that embryos treated at an amplitude of 3 kV, 211 pulses, and 8 cycles at the one-cell stage led to the highest survival and hatching rates. However, the survival and hatching rate ranges for the untreated and electroporated groups decreased from 44-80 to 30-50% and from 38-54 to 24-37%, respectively. Dot blotting and polymerase chain reaction were used to detect the presence of transgenic opAFPGHc in seven-day old fry. Our results revealed a gene transfer success rate of approximately 15%. A Southern blot analysis of fry
Mitochondrial and nuclear DNA reveals a complete lineage sorting of Glossogobius callidus (Teleostei: Gobiidae) in southern Africa

Glossogobius callidus exhibits broad salinity tolerance and is distributed in both estuarine and freshwater environments in southern Africa. Previous studies revealed substantial morphological and molecular variation among populations, suggesting they constitute a species complex. The present study utilised phylogenetic and population structure analyses of molecular sequence data from mitochondrial (cytochrome b) and nuclear (S7 intron 1) DNA markers to evaluate the genetic structure of the species. Two reproductively isolated lineages, 8.7% and 1.1% divergent, respectively, were identified. Lineage 1 represented the true G. callidus distributed mainly among estuarine systems including the type locality (Bushmans River, Eastern Cape, South Africa). Lineage 2 probably represents a cryptic species that is likely to be widespread in tropical and subtropical regions. Pairwise comparisons of both genetic markers within lineages detected high genetic diversity and numbers of private haplotypes. Mozambican haplotypes were divergent (2.7%, cyt b) and restricted to Lineage 2. Both datasets identified a shallow but consistent phylogeographic break between warm-temperate/subtropical and tropical regions. Analysis of Lineage 1 recovered three geographic groups in the warm-temperate region that could be associated with isolation of upper reaches resulting from past river capture and sea level changes. These results are indicative of a complex history of isolation and reconnection in river drainages and/or multiple colonisation events.
Excirolana braziliensis, a Pan‐American sand beach isopod: taxonomic status, zonation and distribution

Excirolana braziliensis Richardson is shown to be the senior synonym of Cirolana salvadorensis Schuster and C. koepckei Bott. The latter two species, incorrectly assigned to Cirolana, were formerly regarded as distinct and were separated on the basis of size-dependent characters. Sampling of sandy beaches along the eastern Pacific from Mexico to Chile (21 localities) and the western Atlantic from Mexico to Brazil, including the West Indies (20 localities), demonstrates that E. braziliensis is commonly the most abundant macroscopic organism present in this habitat. Marked differences in zonation of young and adults are illustrated from data in Panama.
Student‐centred experiments with stream invertebrates

Field experiments are at the core of ecology, yet rarely find their way into education, probably due to a combination of technical challenges and risks associated with fieldwork. This may compromise student education and perception of the subject, making interesting, readily manageable experiments extremely important. We describe how the daily cycle of nocturnal mass movements by river invertebrates (‘drift’) can meet these challenges. The observation of this daily cycle, and simple manipulations using light (to test hypotheses about the triggers for drift) and fine sand (simulating degradation of stream habitats), requires minimal specialist equipment or expertise, yet affords numerous practical benefits and captures student interest through the novel fieldwork. Invertebrate drift illustrates numerous biological principles through investigations adjusted to suit different educational levels.
To Divide or Not to Divide; MicroRNAs and Small Compounds as Modulators of Mitosis

Mitosis is under the stringent quality control of the spindle assembly checkpoint (SAC). However, in cancer cells this control can fail, leading to excessive cellular proliferation and ultimately to the formation of a tumor. Novel cancer cell selective therapies are needed to stop the uncontrolled cell proliferation and tumor growth. The aim of the research presented in this thesis was to identify microRNAs (miRNAs) that could play a role in cancer cell proliferation as well as low molecular weight (LMW) compounds that could interfere with cell division. The findings could be used to develop better cancer diagnostics and therapies in the future. First, a high-throughput screen (HTS) was performed to identify LMW compounds that possess a similar chemical interaction field as rigosertib, an anti-cancer compound undergoing clinical trials. A compound termed Centmitor-1 was discovered that phenocopied the cellular impact of rigosertib by affecting the microtubule dynamics. Next, another HTS aimed at identifying compounds that would target the Hec1 protein, which mediates the interaction between spindle microtubules and chromosomes. Perturbation of this connection should prevent cell division and induce cell death. A compound termed VTT-006 was discovered that abrogated mitosis in several cell line models and exhibited binding to Hec1 in vitro. Lastly, using a cell-based HTS two miRNAs were identified that affected cancer cell proliferation via Aurora B kinase, which is an important mitotic regulator. MiR-378a-5p was found to indirectly suppress the production of the kinase whereas let-7b showed direct binding to the 3’UTR of Aurora B mRNA and repressed its translation. The miRNA-mediated perturbation of Aurora B induced defects in mitosis leading to abnormal chromosome segregation and induction of aneuploidy. The results of this thesis provide new information on miRNA signaling in cancer, which could be utilized for diagnostic purposes. Moreover, the thesis introduces two small compounds that may benefit future drug research.
Detection and identification of antibiotic biosynthesis genes in Bacillus subtilis strains

Two Bacillus subtilis strains L10 and G1, previously isolated from fermented pickles, were tested for antibacterial activity against Vibrio harveyi using a well-diffusion agar assay. Antibiotic biosynthesis genes were then detected in both bacterial strains and included the following genes: bacA, bacB and bacD genes for bacilysin production, ppsE/fenB gene for plipastatin/fengycin production, albF and albA genes for subtilosin production, and srfAB and sfP genes for surfactin production. Based on these results, two B. subtilis strains could be considered as potential biological control agents in aquaculture.
A novel 7·9 kb deletion causing α+‐thalassaemia in two independent families of Indian origin

Summary. We describe the characterization of a novel 7·9 kb deletion that eliminated one of the duplicated α‐globin genes, causing an α+‐thalassaemia phenotype in two independent carriers of Suriname–Indian origin. The molecular characterization of the deletion breakpoint fragment revealed neither involvement of Alu repeat sequences nor the presence of homologous regions prone to recombination, suggesting a non‐homologous recombination event. This α+‐thalassaemia deletion was found to give rise to an atypical haemoglobin H (HbH) disease characterized by a non‐transfusion‐dependent moderate microcytic hypochromic anaemia in combination with a poly adenylation signal mutation of the α‐globin gene (α2 AATAAA → AATA‐‐ ‐‐).
Selective effects of sulfur dioxide and yeast starter culture addition on indigenous yeast populations and sensory characteristics of wine

Riesling musts, with or without sulfur dioxide added, were fermented either with or without the addition of yeast. Uninoculated fermentations took much longer to finish than inoculated musts. There were no significant differences in growth of non‐Saccharomyces yeasts in uninoculated musts with less than 50 mg l−1 SO2 added. The starter culture was completely dominant over indigenous Saccharomyces cerevisiae and strongly inhibitory to non‐Saccharomyces. Alcohol and acetaldehyde were greater in the inoculated treatments ; titratable acidity and acetic acid were greater in the uninoculated fermentations. There were no statistically significant differences among any treatments in final pH, ammonia content, or colour (A420). Uninoculated fermentations had higher sensory scores (P > 0·95) for ‘spicy’, ‘apple’, ‘melon’, ‘pear’, and ‘H2S’, while inoculated wines had higher scores (P > 0·95) for ‘paper’, ‘oxidized’, and ‘sweaty’. Sulfite treatment produced an assortment of significant sensory differences in the finished uninoculated wines, but in inoculated wines the additions of SO2 to the must had no significant effect on indigenous yeast populations or on flavour.
Soil Quality: An Approach to Physical State Assessment

ABSTRACT A method is given to dynamically evaluate the physical aspects of Parr's SOIL QUALITY. Measurements of two main variables are found to be essential: OHI (Optimal Hydric Interval), and RS (Relative Stability of the soil aggregates). The OHI is a range of the hydric content at which available water is easily used by crops, soil solid mass is capable of being drilled by roots and other useful organisms without offering great resistance, and aeration is non-limiting for breathing. The OHI reflects the properties of the “porous structure” of the soil relative to fluid motion and retention, and the consistency of its ped units. The RS informs about the relation of water infiltration capacity values, gaseous exchange, and resistance to erosion for a parcel of cultivated soil, in comparison with another parcel of the same soil kept untouched for a long time. Sensibility of both variables is illustrated through the analysis of real measurements taken in Argiudoll soils of the Argentine Pampean region.
Indirect Interactions in Biological Control of Insects: Pests and Natural Enemies in Alfalfa

The population dynamics of insect pests in agroecosystems may often be linked to those of other phytophagous species through the foraging activities of natural enemies; these indirect interactions provide both opportunities and challenges for biological control. We conducted field experiments to explore indirect interactions in the biological control of the alfalfa weevil (Hypera postica) in northern Utah. Honeydew produced by pea aphids (Acyrthosiphon pisum) in alfalfa fields may be important as a source of nutrition for adults of the wasp Bathyplectes curculionis and may thereby enhance parasitism of the wasp's host, the alfalfa weevil. The presence of aphids may also promote aggregation of lady beetles, which consume weevil larvae in alfalfa. But by feeding heavily on pea aphids as well, these predators could indirectly enhance weevil survivorship by undercutting the wasp's capacity to parasitize its host. In one field experiment, we added pea aphids and/or adults of the lady beetle Coccinella septempunctata to caged field plots of alfalfa during the first (spring) hay crop. Adding aphids increased levels of parasitism among late-maturing alfalfa weevil larvae. Adding lady beetles decreased numbers of late-maturing weevil larvae, but also decreased levels of parasitism among these larvae. In another experiment, repeated application of artificial honeydew to caged alfalfa plots during the first crop increased levels of parasitism among weevil larvae. In a third experiment, a single application of artificial honeydew to open (uncaged) alfalfa plots in mid-May also had a direct positive effect on rates of parasitism among larvae. However, this application had an indirect negative effect on parasitism as well: the presence of artificial honeydew caused aggregation of lady beetles and thus led to decreased aphid abundance. Consequently, provision of artificial honeydew as a food source for parasitoid adults was neutralized by a subsequent reduction in naturally occurring honeydew. These field experiments illustrate the complexity with which indirect interactions can affect exploiter-victim relationships in biological control. They also raise questions con- cerning the long-term consequences that may result from the purposeful introduction of the Old World lady beetle C. septempunctata to alfalfa and other crops in North America. Artificial honeydew may prove useful in enhancing parasitism of the alfalfa weevil, but frequent applications may be required to compensate for associated reductions in availability of naturally occurring aphid honeydew. The effects of honeydew producers on other her- bivores through natural enemies fall under the general concepts of short-term apparent competition and related ecological relationships among species, and highlight the impor- tance of temporal and spatial factors in indirect interactions.
On the genus Golfingia (Sipuncula) in the Plymouth area with a description of a new species

A new species of the genus Golfingia (phylum Sipuncula), belonging to the subgenus Phascoloides Fisher, is described from the Plymouth area. Studies of the local populations of G. (Golfingia) elongata have shown the species to vary considerably in some important taxonomic characters, in particular, the number of retractor muscles: over 13% have only two or three retractors instead of four. Notes on, and a key to, the species of Golfingia found around the British Isles are given.
Effects of Forest Fragmentation on Mortality and Damage of Selected Trees in Central Amazonia

Tropical forests are being cleared at a rate of over 150,000 km 2 per year (Whitmore 1997), causing extensive loss and fragmentation of existing wildlife habitats. Fragmentation has myriad impacts on the dynamics of tropical ecosystems (e.g., Laurance & Bierregaard 1997) but its effects on plant communities have received only limited attention (e.g., Williams-Linera 1990; Laurance 1991, 1997; Malcolm 1994; Turner et al. 1996). We describe the frequency of mortality and damage in trees of the family Myrtaceae in fragmented and continuous Amazonian rainforests. By assessing the relative importance of edge and area effects and fragment age, we can better understand the mechanisms of ecological change in recently fragmented forests.
The evolution of unusual chromosomal systems in sciarid flies: intragenomic conflict and the sex ratio

A model is presented for the evolution of the sciarid chromosomal system. In this model, a driving X chromosome caused female‐biased sex ratios. The drive was exploited by maternal autosomes that segregated with the X at spermatogenesis. Genes in mothers converted some of their XX daughters into sons by eliminating a paternal X from the embryonic soma. L chromosomes were derived from X chromosomes and favored male‐biased sex ratios. An X' chromosome arose that suppressed the effects of L chromosomes. The 1:1 sex ratio is a stalemate between the X' and X'X mothers causing all‐female broods and the L chromosomes in XX mothers causing all‐male broods. Any element (such as an L chromosome) that is preferentially transmitted through one sex will be selected to bias the sex ratio towards this sex.