Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiplex PCR for Identification of Salmonella enterica serovars Typhi and Paratyphi A by Selective Amplification of tyv, prt, viaB, fliC-d and fliC-a Genes

Salmonellosis is responsible for large number of infections in both human and animals. Salmonella enterica serovar Typhi is a causative agent of typhoid fever and Salmonella enterica serovar Paratyphi A is a causative agent of paratyphoid fever. Conventional methods of isolation of Salmonella strains take 4-6 days to complete and are therefore laborious and require substiantial manpower. Therefore development of a PCR assay that can target multiple genes for rapid detection of S. Typhi and S.Paratyphi A. Methods: Synthetic primers for O, H, and Vi antigen genes, tyv , prt , fliC-d, fliC-a, and viaB, were used for the rapid identification of S. Typhi and Paratyphi A with Multiplex PCR. Results: All the clinical isolates examined were accurately identified by this PCR technique, that differentiated S. Typhi and Paratyphi A, based on size and number of amplified fragments. S. enterica serovar Typhi, yielded four bands of tyv(tyvelose epimerase gene, 615bp),prt (paratose gene, 258bp),flic-d(phage-1 flagellin gene for dantigen 750bp) and viaB ( vi antigen gene, 439bp); S.enterica serovar Paratyphi A yielded only two bands prt (paratose gene, 258bp) and flic-a (phage-1 flagellin gene for aantigen 329bp). Conclusion: These data indicate that multiplex PCR is a potentially valuable tool for rapid diagnosis of Salmonella enterica serovar Typhi and Paratyphi A from clinical isolates.
An assessment of radiative heating as a thermal treatment for invasive snakes in cargo

ABSTRACT The brown tree snake (Boiga irregularis) is invasive in Guam and presents a continuous threat of accidental export to new islands in outbound cargo. Current attempts to avoid that scenario rely primarily on canine teams to inspect outbound cargo and vehicles. In prior work, we showed that thermal fumigation could effectively elicit snake exit of cargo under conditions when free flow of air streams is feasible, but this method cannot work with tightly packed cargo. Here we show radiative heating can effectively induce snake exit from cargo refuges at temperatures of 44–48 °C; however, we find passive solar heating of cargo to be unreliable in attaining sufficiently high temperatures for cargo sterilization. Although passive solar radiant heating proved unreliable, an active radiant-heating system has promise as a reliable means of treating tightly packed cargo. Times needed for treatment in a closed, controlled setting are sufficiently short that routine application of the method should provide no serious interruption of normal cargo-handling procedures.
Growth performance of Freshwater prawn Macrobrachium lamarrei lamarrei (H. M. Edward 1837) fed with commercial, supplementary plant and animal feeds

The present study was conducted for period of 45 days to investigate the effect of three different diets on growth performance of Macrobrachium lamarrei lamarrei. Three separate prawn groups of predetermined weight 0.317±0.010g and length 30±. 2mm were fed with three different types of artificially prepared feed Viz, control (commercial feed), supplementary plant feed and supplementary animal feed. The best growth was recorded in animal group fed with supplementary animal feed. The highest mean weight gain and mean length gain were (0.614±0.032g) and (26±2.1mm) in prawns fed with diet-3 (supplementary animal feed). The lowest feed conversion ratio value 0.121±0.141 and highest specific growth rate value 0.594±0.15 % body weight was observed in diet-3 (supplementary animal feed). Further there was a significant difference (P<0.05) in values of condition factor. Lowest value of condition factor 0.555±0.008 was found in diet-3.
Cardiac Effects of Purinergic P2X Channel Activation

Purinergic receptors respond to extracellular nucleotides and their metabolites. They act as important signaling transduction molecules in a variety of biological processes and are important in a number of pathophysiologic conditions that impact human health. A subset of these receptors acts as non-selective cation channels, designated as P2X receptors, which can induce electrical activities in the cellular membrane and thus impact cellular function. A number of longitudinal studies following surgically or genetically induced heart failure animals have demonstrated potential improvement of cardiac function with P2X4 receptor overexpression. We explore here how P2X signaling affects cardiomyocyte excitability and leads to changes in contraction in both computational and experimental models. We confirm computational predictions of P2X induced membrane depolarization and subsequent changes in a number of cardiomyocyte currents using whole cell patch clamp techniques. Direct sodium cxxxentry via P2X channels leading to intracellular ion concentration changes were detected with an increase in Na-K ATPase peak current and enhancement of the calcium entry mode of the Na-Ca exchanger. The latter we show may play a role in the enhancement of contractile response by extracellular ATP. With the aid of computational prediction and interpretation, our findings highlight the value of dynamic considerations of channel currents and offer explanations for prior inconsistencies in the purinergic field. Moreover, we establish an interaction between the P2X4 receptor and nitric oxide production that may underlie its cardioprotective effects after myocardial injury. This improved understanding of P2X action on the heart helps to improve our evaluation of its targeting in clinical applications. Cardiac Effects of Purinergic P2X Channel Activation
Differences in growth and toxicity of Karenia

Differences in Growth and Toxicity of Karenia. (May 2006) Tatum Elizabeth Neely, B.S., University of North Carolina-Wilmington Chair of Advisory Committee: Dr. Lisa Campbell Harmful algal blooms (HABs) in the Gulf of Mexico are primarily caused by dense aggregations of the dinoflagellate species, Karenia brevis. Karenia brevis produces a highly toxic neurotoxin, brevetoxin which has been shown to cause Neurotoxic Shellfish Poisoning (NSP) and respiratory distress in humans in addition to a wide range of negative impacts upon natural ecosystems. Karenia mikimotoi is a co-existing species present during K. brevis blooms. K. mikimotoi has caused major HAB events in other parts of the ocean, but has not been recognized as a major contributor to toxicity of blooms in the Gulf of Mexico. K. brevis and K. mikimotoi have both been associated with the presence of unidentified hemolytic toxins. Production of hemolysins has not previously been investigated for either species to date in the Gulf of Mexico. Presence of hemolysins may affect toxicity and the overall impact of HABs. Therefore, detection of hemolysins is imperative for accurate identification of potential harmful impacts of such blooms. The primary goal of this research is to define whether either species is capable of producing hemolytic activity independent of brevetoxin activity; and to identify if there is significant differentiation between a variety of clonal isolates regarding toxicity and growth rate when subjected to variable experimental conditions.
GC-MS analyses of black cumin essential oil produces with sodium chloride.

The black cumin essential oil and seeds are used in folk medicine, as a bread or cheese flavoring and as a spice in various kinds of meals. In arid and semi-arid regions, where water availability is a major limitation in crop production, using alternative water resources, such as saline water is one way to utilize these barren lands. In this study, we investigate the possible effect of saline irrigation water (SIW) on essential oil (EO) of black cumin an economically important aromatic plant in Egypt. Application of SIW caused a pronounced increment in both EO content and yield. The highest yields of EO (1.1 ml 100 plant-1) obtained from the treatments of 3.1, 4.6 and 6.3 dSm−1. The main constituents of Nigella sativa L seeds EO as detected by GC/MS were p-cymene, α-thujen, β-pinene, γ-terpinene, terpinen-4-ol, thymoquinone and carvacrol which increased as saline irrigation water level increase. Monoterpene hydrocarbons, oxygenated monoterpene and sesquiterpene hydrocarbons were increased as SIW level increase.
CURCUMINOID AND TOXICITY LEVELS OF ETHANOL EXTRACT OF JAVANESE GINGER (Curcuma xanthorriza) ON BRINE SHRIMP (Artemia salina) LARVAE AND ZEBRAFISH (Danio rerio) EMBRYOS

Objective: This study was aimed at determining the levels of curcuminoids and analyzing the toxicity of ethanol extracts of Javanese ginger. Methods: Curcuminoid levels were determined using high-performance liquid chromatography, while the toxicity tests were done on larva of brine shrimp (Artemia salina) by using a brine shrimp lethality test (BSLT) method and embryos of zebrafish (Danio rerio) using a zebrafish embryo acute toxicity (ZFET) method. Results: The level curcuminoid of ethanol extracts was 10.5% dry wt. , consisting of curcumin at the highest percentage (68.06%) followed by desmethoxycurcumin (24.6%) and bisdemethoxycurcumin (1.41%). In BSLT method, the lethal concentration 50% values (LC) value of our ethanol extract was 238 ppm, whereas in ZFET method, the LC value at 96 hours after fertilization was 80 ppm. The ethanol extract of ginger caused major malformations of the pericardial edema of zebrafish embryos at a concentration of 100 ppm. 50 Conclusion: The ethanol extract of Curcuma xanthorrhiza from Bogor contained curcuminoids consisting of curcumin, desmethoxycurcumin, and bisdemethoxycurcumin, with acute toxicity, caused major malformations on the pericardial edema in zebrafish embryos. Keywords: Curcuma xanthorrhiza, Curcuminoid, Toxicity, Zebrafish embryo acute toxicity.50
EFECTO DEL NITROGENO EN EL CRECIMIENTO Y CONTENIDO DE CARRAGENANO EN Gigurtina canalicuhtu HARV. (RHODOPHYTA, GIGARTINALES), EN TANQUES EXTERIORES DE CULTIVO NITROGEN EFFECT ON GROWTH AND CARRAGEENAN CONTENT IN Gigurtinu cunuliculutu HARV. (RHODOPHYTA, GIGARTINALES), IN OUTDOOR TANK CULTURES

Gigaha canaliculata was cultivated under different nutrient conditions in 100-l tanks, to study the effect on growth and yield and quality of carrageenan. The cultures were under four frequenciesof pulse fertilization: every 2, 4, 7 and 14 days, for seven weeks. The doses for each fertilization consisted of 1OO:lO I~M of N03-:P04-2 for three hours. An inverse relationship was observed between growth and carrageenan yield: the highest growth was obsetved in the more fertilized culture (5.5% day-‘), whereas the highest carrageenan yield was observed in the less fertilized culture (49%). Maximum gel strengh was 41 g cm -2 for the more fertilized cultures (two and three times a week). However, there were no significant differences in the sulfate content among the treatments (22%). The different nutrient doses resulted in a differencein carrageenan
Macrophages Are Regulators of Whole Body Metabolism: A Dissertation

i Acknowledgements I would like to sincerely thank my mentor Michael Czech for taking me on as a student, and nurturing my love for science. He has provided guidance and a positive environment that has enabled me to grow as a research scientist. I will take away many lessons from his mentorship, and hope to pay them forward in the future. I would also like to thank my thesis committee for all their suggestions and feedback along the way. The amazing faculty members at UMASS are a major reason why I joined the program and I am grateful for the time and consideration than has gone into assisting me throughout my training. I would also like to thank all members of the Czech lab, both past and present. Especially Myriam Aouadi for her strong mentorship early in the program and who continues to be trusted mentor and friend. Thank you to Rachel Roth Flach and Joe Virbasius for all the help with editing, experimental design and thoughtful discussions. Thank you to for all the excellent teamwork. I am glad to consider you all my lab family and good friends. Finally I would like to thank my friends and family, who in various ways created a support system for me on this journey. Special thanks go to Djade Soumana, Laura Turyatemba, Vladimir Geneus and Caroline Duffy for your friendship and always cheering me on. Thank you to my parents for their love, patience, understanding, and pushing me to realize my true potential. Lastly, ii thank you to my amazing brothers for believing in me and always having my back. Abstract Obesity is the top risk factor for the development of type 2 diabetes mellitus in humans. Obese adipose tissue, particularly visceral depots, exhibits an increase in macrophage accumulation and is described as being in a state of chronic low-grade inflammation. It is characterized by the increased expression and secretion of inflammatory cytokines produced by both macrophages and adipocytes, and is associated with the development of insulin resistance. Based on these observations, we investigated the potential role of macrophage infiltration on whole body metabolism, using genetic and diet-induced mouse models of obesity. Using flow cytometry and immunofluorescence imaging we found that a significant percentage of macrophages proliferate locally in adipose tissue of obese mice. Importantly, we identified monocyte chemoattractant protein 1 (MCP-1) as the stimulating factor. We also found that ATMs can …
Mouse duodenum as a model of inflammation induced by enterotoxigenic Escherichia coli K88

Abstract Introduction: The aim of the experiment was to establish the enterotoxigenic Escherichia coli K88 (ETEC K88)-induced BALB/c mouse duodenum inflammation model. Material and Methods: Mice were administered different concentrations of E. coli K88 (1.0 × 107-109 CFU/mL) for 3 d by means of an esophageal catheter. Results: The results showed that the treated group expressed several significant clinical symptoms, such as reduced dietary demands and weight loss, an increased presence of IL-1α, TNF-α, and MPO in the peripheral blood, and some pathological changes in the duodenum. On the 6th-8th days, the body weight of the mice was the lowest. On the 8th day, there were significant differences in IL-1α, TNF-α, and MPO levels compared to the control group (P < 0.05), the gap between the duodenum mucous layer and the muscular layer had widened, the number of goblet cells was increased, and the inflammatory infiltrate and inflammation changes in the lamina propria and the mucous layer were the most obvious. Conclusion: The duodenum inflammation was the most severe on day 8; thus, the model was successfully established. In addition, varying concentrations of ETEC K88 did not significantly influence the duodenum inflammation (P > 0.05).
New insights into Plutonium, one of the largest and least known European centipedes (Chilopoda): distribution, evolution and morphology

Plutonium zwierleini is one of the largest scolopendromorph centipedes in Europe and is known for debates on the evolution of segmental body pattern in arthropods. However, only 24 records have so far been reported and probably only a dozen specimens still exist in collections. Based on 19 new data from professionals and amateur recorders, we confirmed that populations are present today in four disjunct areas: southern Iberian Peninsula, Sardinia, southern Italian Peninsula and Sicily. A phylogenetic analysis of the first molecular data obtained for Plutonium (16S, COI, 18S, 28S) provided strong evidence that it is closely related to Theatops, either sister to the latter or nested within it, with an estimated separation since the Mesozoic. By examining specimens of Plutonium from all the four inhabited areas and specimens of most of the species of Theatops, we also documented many synapomorphies uniting Plutonium and Theatops (brown-orange colour, whitish patches replacing the ocelli, a particular denticulation on the forcipules, conspicuously swollen and piercing ultimate legs) and some derived characters unique to Plutonium, including the blade-edged claws of the ultimate legs and the previously overlooked presence of long, dense setae on most other legs, in both sexes and in the entire species range.
One Century of Interactions Between Intensive Breeding and Genetic Diversity Conservation of Barley

The footprint left by one century of intensive breeding on the phenotype and genotype has been studied in barleys that originated and were developed at the territory of Moravia and south-western Slovakia. The set of barleys ( Hordeum vulgare L.) used in retrospective analysis included 106 landraces, obsolete and modern cultivars from the period 1900-2003. The one-hundred year breeding effort resulted to crucial changes of agronomic and technological parameters. The number of spikes m -2 , spike density, protein and starch contents were significantly (P<0.05) different in new barleys (developed after the year 1972). Improvement of malting quality was through decreasing of proteins (average annual decline 0.034% year -1 ) and increasing of starch (average annual gain 0.074% year -1 ) in grains. Change in genetic diversity has been studied at 27 microsatellite loci with conclusion that nothing adverse happened at these loci during one century of breeding. The oldest barleys were heterogeneous populations, the modern ones were more homogeneous, and moreover introduction of new germplasm within the breeding process has brought new microsatellite alleles. Both, the total number of alleles and average number of alleles per locus indicated that molecular diversity was not reduced by long-term breeding. However, the average number of alleles per genotype pointed to the existence of genetic erosion caused by the gradual replacement of original landraces and local cultivars by modern cultivars. The index of genetic diversity reflected that reduction of genetic diversity from the thirties to the seventies has been turned by breeders in the eighties of the 20 th century.
Managing trap‐nesting bees as crop pollinators: Spatiotemporal effects of floral resources and antagonists

Summary 1.The decline of managed honeybees and the rapid expansion of mass-flowering crops increase the risk of pollination limitation in crops and raise questions about novel management approaches for wild pollinators in agroecosystems. Adding artificial nesting sites, such as trap nests, can promote cavity-nesting bees in agroecosystems, but effectiveness could be limited by the availability of floral resources in the surrounding landscape and by natural antagonists. 2.In two European regions, we exposed artificial trap nests in paired field boundaries adjacent to oilseed rape (OSR) fields or non-flowering crops for two years within 32 landscapes covering two independent gradients of OSR cover and semi-natural habitat (SNH) cover in the landscape. We analysed the effects of local and landscape-wide floral resource availability, land-use intensity, landscape complexity and natural antagonists on community composition and population dynamics of trap-nesting bees. 3.Number of brood cells showed a strong, three-fold increase in response to the additional nesting sites. Species richness and abundance of cavity-nesting bees that were active during OSR flowering increased significantly with increasing amount of early-season landscape-wide floral resource availability, such as the cultivation of OSR. Later foraging species benefited instead from the availability of late-season alternative flower resources or SNH cover once the mass-flowering had ceased. Density-dependent parasitism increased following mass-flowering, while no density-dependent effect was found during mass-flowering. 4.Structural equation modelling revealed that the influence of floral resource availability on community growth rate was mediated by community size. Community size showed a strong negative effect on community growth rate. Despite positive density-dependent parasitism, antagonists had only weak regulating effects on community growth rate. 5.Synthesis and applications. Trap-nesting bee populations grow markedly with the increasing availability of food resources in the landscape and effectiveness of trap nests is only marginally limited by natural antagonists. Thus, trap nests could be a simple pollinator-supporting strategy to accompany the current expansion of mass-flowering crops, and to ensure pollination services for insect-pollinated crops. Trap nests benefit not only early season active generalist bees during oilseed rape flowering but also species with later phenology if accompanied by other pollinator-supporting practices. This article is protected by copyright. All rights reserved.
Characterising the development of the understanding of human body systems in high-school biology students – a longitudinal study

ABSTRACT Science education today has become increasingly focused on research into complex natural, social and technological systems. In this study, we examined the development of high-school biology students’ systems understanding of the human body, in a three-year longitudinal study. The development of the students’ system understanding was evaluated using the Components Mechanisms Phenomena (CMP) framework for conceptual representation. We coded and analysed the repertory grid personal constructs of 67 high-school biology students at 4 points throughout the study. Our data analysis builds on the assumption that systems understanding entails a perception of all the system categories, including structures within the system (its Components), specific processes and interactions at the macro and micro levels (Mechanisms), and the Phenomena that present the macro scale of processes and patterns within a system. Our findings suggest that as the learning process progressed, the systems understanding of our students became more advanced, moving forward within each of the major CMP categories. Moreover, there was an increase in the mechanism complexity presented by the students, manifested by more students describing mechanisms at the molecular level. Thus, the ‘mechanism’ category and the micro level are critical components that enable students to understand system-level phenomena such as homeostasis.
Polyploidy as a Factor in the Evolution of the Bouteloua curtipendula Complex (Poaceae: Chloridoideae)

Abstract In this paper we assess the impact of polyploidy and hybridization in the Bouteloua curtipendula species complex (BCC). The BCC is a monophyletic group of perennial grasses in the Chloridoideae subfamily. We tested for evolutionary signatures of hybridization and polyploidy in the BCC by obtaining 77 chromosome counts from anther mother cells (2n = 20 to >100) and comparing the phylogenetic pattern of diploids and polyploids in nuclear and chloroplast trees. We sequenced ITS and trnT-L-F regions for 96 and 70 individuals, respectively, resulting in 150 nuclear ribosomal ITS sequences, including 54 cloned sequences. We found no evidence for recombination between ITS sequences with a PHI test. Maximum parsimony and Bayesian analyses were used to estimate the ITS phylogeny. Diploid samples were found in all clades, while most of the polyploid samples were concentrated in a single clade. Cloned diploids contained one to three copies of ITS with >99% sequence similarity. The tetraploids B. purpurea and some B. curtipendula samples had a low amount of variation among ITS copies, while the cloned polyploids possessed several highly divergent ITS copies. Pollen size correlates with ploidy-level in the BCC, but is not a clear indicator of genome size. We found evidence that the BCC lineage has a complicated evolutionary history that has included autopolyploidy and allopolyploidy.