Miracle-dz/UniFAR-FTUs huggingface dataset:
Iron homeostasis is hierarchically regulated by multiple inputs : evidence for the role of reactive oxygen species and iron-zinc cross talk

Iron (Fe) is an essential nutrient for all forms of life, but excess Fe is capable of damaging biomolecules through peroxidation by reactive oxygen species (ROS). Cadmium (Cd) is a toxic non-essential element which is also capable of inducing ROS and also has been found to induce an Fe deficiency-like response, presumably by inhibiting Fe uptake. Here, we used Cd to probe the extent on Fe deficiency responses in wildtype plants Col and in an Fe over accumulating mutant (opt3-2). Our results demonstrate that Cd induces a conserved set of Fe deficiency responsive genes in leaves. This include regulators of Fe deficiency in companion cells which in turn transduce a Fe deficiency signal to roots. Interestingly, some of these Fe deficiency genes failed to be induced by Cd in opt3-2, presumably due to the presence of excess Fe. Moreover, we found that the combination of Fe excess and Cd substantially elevates ROS levels. ROS thus triggering additional changes in the leaf and root transcriptional programs. Despites this increase in ROS, a select cluster of Fe deficiency markers in leaves was found to remain induced by Cd, independently of the presence of excess Fe or high ROS, suggesting that in this case Cd interferes directly with Fe sensing. We further implicate the chloroplast as one site of the generation of these ROS, as determined by a dramatic decrease in photosynthetic efficiency in opt3-2 after Cd exposure. Altogether, our data points to a hierarchical regulation of Fe deficiency responses based on multiple inputs, including the perceived global Fe status, the levels of ROS within tissues, and a sensing core unique to leaves, which is particularly labile in the presence of cadmium.
The Effect of Habitat-Forming Bryozoans on Biodiversity

Bryozoans form complex habitat when high densities of heavily-calcified colonies grow to > 5 cm in three dimensions. Such habitat is found on hard and soft substrata; at shallow subtidal and shelf depths; where currents are strong but wave action is low; where sedimentation is low; and in polar, tropical, but most commonly temperate waters. Habitat-forming bryozoans support diverse assemblages of macroinvertebrates, but are damaged by anthropogenic activities, particularly commercial fishing of the seafloor using mobile gear. Bryozoan-generated habitat is unusually common in New Zealand waters. Presence-only habitat suitability models were developed for a suite of habitat-forming bryozoan species that occur in New Zealand. These models require testing and refining, but provide a useful tool for generating hypotheses about the historical distributions of habitat-forming bryozoans. Comparisons between the models and existing literature raised the possibility of undiscovered areas of bryozoan-generated habitat. Data describing the distribution of commercial fishing suggests that if bryozoan-generated habitat was present it is likely to have been destroyed, highlighting the need to understand how changes to habitat complexity affect benthic biodiversity. A mensurative study of macroinvertebrate assemblages associated with bryozoan-generated habitat was carried out on Otago shelf, south-eastern New Zealand. Variables describing the amount of epibenthic habitat and the diversity of sediment components were particularly important in explaining the various biodiversity metrics. Habitat complexity resulted from the growth and taphonomy of several species, particularly Cinctipora elegans. The abundance of macroinvertebrates associated with habitat-forming bryozoans drove changes in the assemblage structure (i.e. the passive sampling hypothesis of the species-area relationship, or SAR). Additionally, complex habitats increased habitat diversity, providing for specialist taxa (the habitat diversity hypothesis). No thresholds were identified in correlations between habitat complexity variables and biodiversity metrics, suggesting any reduction in complexity would negatively affect benthic biodiversity. To investigate further the relative importance of the SAR and to identify which elements of habitat structure were most important to associated fauna, PVC mimics of Cinctipora elegans were deployed on Otago shelf for six months. There were significant differences in assemblage structure and composition in relation to mimic branch density. Rarefaction and estimated total richness illustrated the strong effect of surface area on richness, but a small residual effect of habitat complexity
Effects on Survival, Reproduction and Growth of Ceriodaphnia dubia following Single Episodic Exposure to Copper or Cadmium

Effects of episodic exposures have gained attention as the regulatory focus of the Clean Water Act has shifted away from continuous-flow effluents. Standardized laboratory toxicity tests require that exposure be held constant. However, this approach may not accurately predict organism responses in the field following episodic exposures such as those associated with rain-driven runoff events or accidental pollutant discharge. Using a modified version of the 7-day short-term chronic test recommended by the US Environmental Protection Agency, Ceriodaphnia dubia were exposed to copper or cadmium for durations ranging from 1 minute to 24 hours. In addition, adult reproductive recovery and effects on second generation individuals was assessed following select copper exposures. Finally, cadmium exposures were compared in reconstituted hard water (RHW) and municipal treated wastewater effluent (TWE). Following exposure, organisms were transferred to clean RHW or TWE and maintained for the remainder of the test. No- and lowest observed effect concentrations (NO- and LOECs) increased logarithmically with respect to logarithmic decreases in duration regardless of metal, endpoint or water type. Effective concentrations of cadmium however, were usually higher than those of copper, especially in TWE. LOECs for C. dubia survival following 24-hour and 5-minute exposures to copper were 116 and 417 µg/L, respectively. LOECs for fecundity were 58 and 374 µg/L, respectively. Neonate production of first generation adult C. dubia appeared to recover from pulsed copper exposure upon examination of individual broods. Cumulative mean neonate production however, showed almost no signs of recovery at exposure durations ≥3 hours. Pulse exposure to copper also resulted in diminished fecundity of unexposed second generation individuals. Such effects were pronounced following parental exposure for 24 hours but lacking after parental exposures ≤3 hours. LOECs for C. dubia survival following 24-hour and 5-minute exposures to cadmium in RHW were 44 and 9000 µg/L, respectively. LOECs for fecundity were 16 and 5000 µg/L, respectively. In TWE, LOECs for C. dubia survival were 83 and >10,000 µg/L, respectively. LOECs for fecundity in TWE were 48 and 7000 µg/L, respectively. Runoff pollution is site and event specific, however, data presented herein may be useful as a predictive tool under various conditions.
Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupins

Les genomes sont des structures dynamiques, variant en taille et en composition, dans lesquelles les retrotransposons jouent un role moteur. Dans ce cadre, nous nous sommes fixe trois objectifs de travail : 1) ameliorer notre connaissance des relations phylogenetiques au sein du genre Lupinus (Fabaceae) par l'utilisation de nouveaux marqueurs nucleaires (ARNr-ETS et SymRK), 2) evaluer par amplification et par hybridation in situ la diversite, l'abondance et le role des retrotransposons Ty1/copia et Ty3/gypsy dans les variations de taille de genome des lupins, et 3) sequencer, annoter et comparer une premiere region genomique disponible pour un lupin avec les regions homologues d'autres fabacees. La phylogenie obtenu ameliore notre comprehension de l'histoire evolutive des lupins, et met en evidence des schemas de variation de taille de genome differents d'une lignee a l'autre. Les analyses de retrotransposons revelent que les elements copia et gypsy contribuent de facon plus significative aux differences de taille de genome chez les lupins mediterraneens que chez les lupins africains et suggerent differents modes et mecanismes d'evolution de la taille des genomes au sein du genre. A l'echelle locale (region du gene SymRK), nous confirmons la forte implication de ces elements qui representent 25% de la region analysee chez Lupinus angustifolius.
Stimulating Effects of Far-infrared Ray Radiation on the Release of Antioxidative Phenolics in Grape Berries

This research was conducted to determine the effect of far-infrared ray (FIR) irradiation of grape berries as a potential application for manufacturing grape products with a high amount of antioxidant chemicals. Two grape cultivars, the red grape cv. Campbell Early and the white grape cv. Thompson Seedless, produced increased amounts of crude extracts, in the FIR treatments compared to a non-FIR treatment control with same temperature. However, total phenolic concentrations and antioxidant activity in a ‘Campbell Early’ increased in the extracts following FIR treatment, whereas those of ‘Thompson Seedless’ did not increase significantly. High performance liquid chromatography (HPLC) analysis indicated that functional components affecting antioxidant activity were significantly increased in the extract of ‘Campbell Early’ following FIR treatment. Our results indicate that application of FIR treatment in heat process of grapes increases levels of antioxidative phenolic chemicals and it may help to enhance the availability of antioxidative compounds in various grape food products.
Analisis Keragaman Komunitas Bakteri pada Lambung Madu Lebah Apis mellifera, Apis cerana, dan Tetragonula laeviceps

FITRI ROSADELA. Analysis of Communities Bacterial Diversity on Bees Honey Stomach from Apis mellifera, Apis cerana, and Tetragonula laeviceps. Supervised by IMAN RUSMANA and RIKA RAFFIUDIN. Bees are one of the pollinators that a honey producing agent as well. Honey derives from nectar that stored and procees in honey stomach. The quality of honey is determined by physical, chemical and microbes in the honey stomach as well. Previously bacteria that found in bees honey stomach of Apis mellifera, Apis cerana, and Tetragonula laeviceps are lactic acid bacteria (BAL). This study were aimed to analyze the diversity of bacterial communities (bacterial metagenom) derived from bees honey stomach of A. mellifera, A. cerana, and T. laeviceps using Denaturing Gradient Gel Electrophoresis (DGGE) method. Previous researches of bacterial communities are more focused on the entire digestive tract, which is not specifically in honey stomach of the bees. A total of 6 samples with different honey stomach numbers were taken from A. mellifera, A. cerana, and T. laeviceps. The diversity of bacterial communities showed differences among three bees species. The number one of A. cerana has the highest number of OTUs (15 OTUs) compared to the other sample. While the T. laeviceps number two show the highest percentage of OTU dominant at 59.4%. The bacterial community in bees honey stomach of A. mellifera, A. cerana, T. laeviceps shows the similarity of bacteria from phylum Firmicutes, Proteobacteria, Acidobacteri and Fusobacteria. Actinobacteria and Bacteroidetes phyla are found only in A. cerana honey stomach.
The pollination biology and breeding system of Banksia spinulosa

Mating systems are of fundamental importance in any consideration of the dynamics of plant populations, since patterns of mating determine the transmission of genes in a population, and thus have a major influence on the structure and dynamics of populations. Moreover, plant reproduction is influenced by events which occur throughout the mating process. Factors such as flowering patterns, pollinator effectiveness and behaviour, population structure, and incompatibility mechanisms are important determinants of mating patterns. Any quantitative and definitive assessment of plant mating systems therefore requires an integrated approach, which encompasses these factors. This study used such an approach to investigate the mating system of one species of Banksia. The reproductive biology of a population of Banksia spinulosa was studied in detail at a site within Barren Grounds Nature Reserve near Wollongong. Several important aspects of the reproductive biology of this species were investigated, including; (i) flowering and fruiting patterns, (ii) pollinator visitation and behaviour, (iii) the mating system and genetic structure of the population and (iv) the potential for choice in the
Improved Retroviral Vectors for Gene Transfer and Expression

We describe a set of murine retrovirus-based vectors that include unique cloning sites for insertion of cDNAs such that the cDNA can be driven by either the retroviral long terminal repeat, the immediate early promoter of human cytomegalovirus, or the simian virus 40 early promoter. The vectors carry the neomycin phosphotransferase gene expressed from an alternate promoter as a selectable marker. These vectors have been constructed to prevent viral protein synthesis from the remaining viral sequences, to yield high-titer virus stocks after introduction into retrovirus packaging cells, and to eliminate homologous overlap with viral DNAs present in retrovirus packaging cells in order to prevent helper virus production. Methods for generating high-titer virus are described.
Fossil Fuels Consumption, Carbon Emissions, and Economic Growth in Indonesia

Environmental issues have become an issue of recent interest due to climate change associated with increased levels of pollution and degradation of environmental quality as a result of increased human economic activity. This paper discusses the relationship between fossil fuel consumption, carbon dioxide emissions, and economic growth, the impacts of energy conservation, as well as the projection of energy mix in Indonesia by applying Vector Error Correction Model (VECM) Granger causality, and Long-run Energy Alternative Planning (LEAP). Empirical results show that in the short-run there are unidirectional Granger causalities running from coal consumption to output (growth hypothesis) and from output to oil consumption (conservation hypothesis). However, in the long-run the results suggest unidirectional Granger causality only running from oil consumption to output and carbon emissions. The projection results show that the result of LEAP Projection based on National Master Plan for Energy Conservation (RIKEN) 2005 target has a lower energy saving rate (17.32 percent) compared to the Vision 25/25 target (18 percent).
Quality Control and Captive Rearing Genetics of the Biological Control Agent Trichogramma pretiosum

In these studies, we determined the quality of Trichogramma parasitoids reared in several Mexican insectaries, evaluated the clonal variability found in Trichogramma pretiosum populations where the infection has gone to fixation, and determined the potential for genetic changes taking place during mass rearing of Trichogramma spp. The results showed that there is substantial potential for adaptation to mass rearing conditions when mass reared populations are initiated with genetically variable populations. In addition, we determined that inbreeding depression is possible even in species such as Trichogramma pretiosum where their sex determination and normal sibmating mating system would predict a minimal effect of inbreeding. With respect to the quality of mass reared Trichogramma , we found discrepancy between the reported and the reared specie, presence of unnoticed species replacement, and we found that the reared species barely met the minimum standards suggested by the international organization for biological control/ European community. From the PI-Wolbachia infected population, we found a surprisingly large amount of variability among the different clonal lines when life history measurements were made. In this dissertation, we also outlined several guidelines for insectaries regarding how to maintain high field quality of the natural enemies they produce. Finally, our findings of the high diversity of clones in entirely asexual populations may result in a more rational future use of asexual wasps in biological control.
Structural Studies of a Xyloglucan Endotransglycosylase from Populus tremula x tremuloides and Three Conserved Hypothetical Proteins from Mycobacterium tuberculosis

A large fraction of the Mycobacterium tuberculosis genome codes for proteins of unknown function. We here report the structure of one of these proteins, Rv0130, solved to a resolution of 1.8 angstrom. The Rv0130 monomer features a single hotdog fold composed of a highly curved beta-sheet on top of a long and a short alpha-helix. Two monomers in turn pack to form a double-hotdog-folded homodimer, similar to a large group of enzymes that use thiol esters as substrates. Rv0130 was found to contain a highly conserved R-specific hydratase motif buried deeply between the two monomers. Our biochemical studies show that the protein is able to hydrate a short trans-2-enoyl-coenzyme A moiety with a k(cat) of 1.1 x 10(2) sec(-1). The importance of the side chains of D40 and H45 for hydratase activity is demonstrated by site-directed mutagenesis. In contrast to many hotdog-folded proteins, a proline residue distorts the central helix of Rv0130. This distortion allows the creation of a long, curved tunnel, similar to the substrate-binding channels of long-chain eukaryotic hydratase 2 enzymes.
The Effect of Cosmetics Curation Service Quality Attributes on Consumer’s Intention to Use

In modern society, the means of sharing information has expanded from existing personal computers and mobile devices to a variety of smart devices rapidly increasing information production. Recently, curations have extended to online businesses. There has been wide use of curation services in the cosmetics curation market. In this study, focuses on factors which cosmetics curators have in mind. In relation to the impact of cosmetics curation quality properties on usability, the effects of the medium of satisfaction and confidence are to be verified. For this study, a survey of 378 women in their 20s and 40s who had experience with curations was done and the collected data were analyzed using SPSS 23.0 and AMOS 23.0 statistics programs. The results showed that information quality and personalization quality of cosmetics curation service were important factors affecting customer satisfaction. Personalization quality also had a positive effect on trust. System quality has a positive impact on trust and further influence on intention to use. This indicates that the trust on the curation service depends on the stability of system. However, design quality was found to have no significant effect on satisfaction and trust. In future, the research related to application and utilization of big data-based cosmetic curation will be further expanded.
Cercospora and Cercosporidium Tolerance to Benomyl and Related Fungicides in Alabama Peanut Fields

Cercospora arachidicola [Mycosphaerella arachids] and Cercosporidium personatum [M. berkeleyi] isolates from commercial groundnut fields in Ala. tolerated levels of benomyl and related fungicides X 10 those previously recorded. No tolerance was found in a field that had not previously been treated with these compounds
Variance components and genetic parameter estimates using random regression models on test day milk yields of Holstein Friesians.

considered in genetic evaluation systems of dairy cows for a long time. Nowadays, the use of 305 day lactation records have replaced by consideration of test day records using test day models as repeatability, multivariate and random regression models which have been developed to model test day records directly . In repeatability model, test day records are considered as repeated observations of same trait but in multivariate model, test day records are considered Kafkas Univ Vet Fak Derg 15 (4): 547-551, 2009 RESEARCH ARTICLE
Genetic profiling of Plasmodium ovale wallikeri relapses with microsatellite markers and whole-genome sequencing

Like Plasmodium vivax, both Plasmodium ovale curtisi and Plasmodium ovale wallikeri have the ability to cause relapse in humans, defined as recurring asexual parasitaemia originating from liver dormant forms subsequent to a primary infection. Here, we investigated relapse patterns in P. ovale wallikeri infections from a cohort of travelers who were exposed to the parasite in Sub-Saharan Africa and then experienced relapses after their return to France. Using a novel set of eight highly polymorphic microsatellite markers, we genotyped 15 P. ovale wallikeri relapses. For most relapses, the paired primary and relapse infections were highly genetically related (with 12 being homologous), an observation that was confirmed by whole-genome sequencing for the four relapses we further studied. This is, to our knowledge, the first genetic evidence of relapses in P. ovale spp.
Your Children Mite Not be Safe at School: An Outbreak of Biting Rat Mites at a Southern California Elementary School Campus

Author(s): Morgan, Timothy; Krueger, Laura; Cummings, Robert; Simms, Jerry | Abstract: During May, 2017, the Orange County Mosquito and Vector Control District (OCMVCD) received anonymous calls from distressed school staff and parents of children attending an elementary school (Villa Park Elementary School, VPES) in Orange County, California, about an outbreak of pruritic dermatitis that was believed to be caused by biting arthropods. The incident received intense media coverage and led to a partial closure of the campus. With no identified culprit, OCMVCD interviewed VPES staff and surveyed the school property for vertebrate pests and their ectoparasites to determine the source of the outbreak. After thorough inspections of the exterior and interior of classrooms and a carefully-placed, glue-board trap survey, OCMVCD detected signs of significant roof rat activity (feces, rub marks, and harborage sites) throughout the campus and the presence of rat mites inside multiple classrooms. OCMVCD worked with other governmental agencies (Orange County Health Care’s Environmental Health, California Department of Pesticide Regulation’s School Integrated Pest Management Program, local city officials) and the VPES administration to educate parents about the vertebrate pests on the school grounds and the complexities of controlling the rat mite infestation during the school year. OCMVCD also identified deficiencies in the school’s pest control program and developed an integrated vector management plan to address the immediate and long-term health threats to prevent rodent and rat mite outbreaks in the future. This report details the investigation and methodology used to locate and eradicate the vertebrate and ectoparasite threats on the VPES campus and the challenges encountered during the process.
Isolation of endophytic plant growth promoting Burkholderia sp. MSSP from root nodules of Mimosa pudica

Endophytic bacteria reside within plant tissues and have often been reported to promote plant growth. Rhizobia are particularly known for their symbiotic relationship with legumes. A bacterial strain MSSP was isolated from surface-sterilized root nodules of Mimosa pudica. MSSP was Gram-negative, capsulated, motile, non-endospore forming rod with free nitrogen (N) fixation ability. Unlike N-fixing bacteria forming symbiotic relationship with legumes that largely exist in α-subclass of proteobacteria, MSSP belongs to β-class of proteobacteria. Phylogenetic analysis of 16 S rDNA demonstrated that MSSP belongs to the genus Burkholderia. This isolate secretes phytohormone, ACC deaminase, solubilizes phosphate and is antagonistic against phytopathogens.