Miracle-dz/UniFAR-FTUs huggingface dataset:
The antimicrobial activity of cumin, thyme and anise extracts on some pathogenic and food spoilage bacteria

The cold and hot water extracts of Cumin (Cuminum cyminum), Thyme (Thymus vulgaris) and Anise (Piminella anisum) were examined for their antimicrobial activity against some food borne pathogens such as Escherichia coli, Salmonella typhimurium and Staphylococcus aureus subsp. aureus and food spoilage bacteria such as Bacillus cereus and B. stearothermophilus. The hot extraction method of the used plant parts gave a pronounced inhibition effect as well as bactericidal activity more than the cold extraction method. It was found that hot water extracts of cumin and thyme have the strongest inhibition effect on E coli, S. typhimurium and Staph. aureus subsp. aureus when experimented by disc diffusion assay method. Moreover, E. coli was also strongly inhibited by the hot water extract of anise. On the other hand, B. cereus and B. stearothermophilus were slightly inhibited by hot extract of cumin and thyme. Whereas, Anise extracts show no inhibition effect on Staph. aureus subsp. aureus, B. cereus and B. stearothermophilus. The extracts which exhibit strong inhibition effect were examined for their bactericidal activity by using of kill curve method. It was found that cumin and thyme extracts have bactericidal effect on E. coli, S. typhimurium and Staph. aureus subsp. aureus. While, Anise extract has bactericidal effect only on E. coli.
Complete mitochondrial genome and the phylogenetic position of Halcyon smyrnensis (Aves: Coraciiformes)

Abstract The complete mitochondrial genome of Halcyon smyrnensis was determined in this study. The mitogenomic length of Halcyon smyrnensis was 17 318 bp, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Phylogenetic analyses show that H. leucocephala, H. pileata and H. smyrnensis congregated together, and our sample was sister to H. pileata.
Muscle protection during hibernation of Daurian ground squirrels (Spermophilus dauricus): role of atrogin-1, MuRF1, and fiber-type transition

We investigated the mechanism of protection from skeletal muscle atrophy in the hind limb extensor digitorum longus (EDL) muscle of hibernating Daurian ground squirrels (Spermophilus dauricus Brandt, 1843). The effects of unrestrained hibernation and 14 day hind limb unloading (HLU) on EDL were studied in three seasons (summer, autumn, and winter). Atrogin-1 and MuRF1 mRNA skeletal muscle expression, wet muscle mass, and muscle to body mass ratios were unchanged during hibernation in all three seasons. EDL mass measurements decreased following HLU and atrogin-1 and MuRF1 mRNA expression increased. In summer, atrogin-1 and MuRF1 mRNA expression increased by 85% and 75%, respectively; in autumn, by 95% and 69%, respectively; and in winter, by 91% and 65%, respectively (P < 0.05). In the HLU group, microscopic skeletal muscle changes were present, including a reduction in the percentage of type-I skeletal muscle fibers. Fat storage in Daurian ground squirrels and a shorter photoperiod during hibernation did .
The effect of elevation and time on mountain spider diversity: a view of two aspects in the Cederberg mountains of South Africa

Our aim is to test if long‐term patterns in α alpha and β beta diversity along an elevational transect on two aspects of a mountain are consistent through time using spiders as model organisms, quantify the role of elevation and time (seasonal and inter‐annual) in explaining these patterns and partition the relative contribution of nestedness, species turnover and species loss in explaining these diversity patterns.
Dynamic group size and displacement as avoidance strategies by eiders in response to hunting

Hunting by humans constitutes a major source of mortality that selects for avoidance strategies. Group formation in eiders Somateria mollissima in response to hunting from motorboats was studied in the Danish Wadden Sea as an avoidance strategy to humans. In autumn the birds' food demand and energy consumption are relatively low and the need for optimal feeding opportunities are not as essential as during winter. We tested the hypothesis that eiders aggregate in groups of variable size dependent on predation risk (hunting), season and site. During autumn at the preferred feeding sites eiders occur in small numbers and group size increase together with hunting activity. Opposite during winter, eiders occur in large numbers and group size decrease when hunting activity increase. Hunting activity displaced eiders to adjacent sites with no or low hunting intensity and low food availability where group size of eiders increase during both autumn and winter in relation to the overall hunting activity. The formation into larger groups when hunting activity increase is probably due to increasing effects of vigilance and dilution, whereas formation into smaller groups is assumed to reduce the eiders conspicuousness to hunters. This change in group size made it possible for eiders to forage in areas with high food availability and high hunting intensity, while minimizing the risk of being detected by hunters. When the largest numbers of hunters were present at the preferred feeding site, group sizes during both autumn and winter were 110–125 eiders, indicating an optimal group size in relation to hunting density. Eiders located outside preferred feeding sites were in poorer body condition, suggesting that displacement was a suboptimal decision caused by hunting. We conclude that eiders adopted regrouping and displacement as two different strategies during hunting. Both strategies are tradeoffs between the risks of being detected by hunters and killed, and the benefits of feeding on mussel stocks thereby increasing body condition and hence fitness.
Inherently slow growth in two Caribbean epiphytic species: A demographic approach

In relation to the drought-prone and nutrient-poor habitat, vascular epiphytes are routinely referred to as inher- ently slow-growing plants, although actual evidence is rare. To test this notion we measured in situ growth of the understorey orchid Aspasia principissa and the tank bromeliad Vriesea sanguinolenta, and, for the latter species, also the growth under favourable conditions in the greenhouse. Using growth analysis we show: (1) that in an intraspecific comparison, small to intermediate individuals yield the highest relative growth rates (RGR) in situ: A. principissa: 1.6 10-3 d-1; V. sanguinolenta: 3.3 10 -3 d -1 ; (2) that the bromeliad reaches maximum size after ca. 15 yr, while the orchid needs at least 20 yr; and (3) small V. sanguinolenta plants exhibit a highly plastic growth response to favourable conditions in the green- house, reaching an almost 10-fold increase in RGR. In spite of a substantial increase in growth under more favourable condi- tions, our results are consistent with the notion that epiphytes are inherently slow growing organisms.
Influence of leaf litter composition on ant assemblages in a lowland tropical rainforest in Thailand.

In tropical rainforests, variability in the distribution of soil and litter arthropods is usually explained at regional scales by altitude, soil nutrients, and disturbance regimes. However, the influence of these factors on insect assemblages at the micro-habitat scale has rarely been studied. We investigated whether the species identity of decomposing leaves in tropical forest affected the composition of ant assemblages around them. Ants were extracted from litter below three common tree species, Parashorea stellata (Dipterocarpaceae), Intsia palembanica (Fabaceae) and Shorea gratissima (Dipterocarpaceae) in a 24 ha lowland rainforest plot in southern Thailand. A total of 2,257 individual ants, representing 71 species in 38 genera of 6 subfamilies were collected in the dry and wet seasons during 2010. Ant species richness was never significantly different among litter samples under the crown cover of three tree species. Ant species richness was higher in the wet season than the dry season. Our results demonstrate that ant assemblages are seasonally heterogeneous. Leaf mass and litter mass did not relate to the presence of ant diversity. Soil humidity was the only important factor influencing ant diversity in this study. Future studies should consider the importance of soil moisture related to litter ant diversity.
THE AFRICAN NANNOMYS (MURIDAE): AN EARLY OFFSHOOT FROM THE MUS LINEAGE—EVIDENCE FROM scnDNA HYBRIDIZATION EXPERIMENTS AND COMPARED MORPHOLOGY

ABSTRACT The systematics of the African pigmy mice Nannomys is studied through molecular and morphological approaches. Molecular data based on single-copy nuclear DNA (scnDNA) hybridization indicate that Nannomys is as divergent from Mus sensu stricto as is the Asian subgenus Coelomys; moreover, it shows a much closer relationship to Mus than to any other African, Oriental, or Palearctic murid genus tested so far. Furthermore, when using a molecular clock calibrated by Mus/Rattus split, estimated by paleontologists at about 10 million years ago, it appears that the separation between Nannomys and the Mus lineage occurred about 5 million years ago, a date which could indicate the earliest entry of the ancestors of Nannomys in Africa. Morphological investigations indicate that it is almost impossible to distinguish between Nannomys sp. and some similar Asian Mus species. These results suggest that Nannomys and their Oriental relatives have a common ancestor either in Africa or in Asia, or else have develope.
Pre-conditioning of fermenting yeast with sodium chloride for ethanol production

Three Saccharomyces cerevisiae strains (MTCC 11815, D-7 LALVIN and Y-2034) were sequentially preconditioned on synthetic medium containing (2-10 % w/v) NaCl and 4% (w/v) concentration of NaCl was found to be optimum for preconditioning in terms of viable and non-viable cell counts for S cerevisiae (MTCC 11815 and D-7 LALVIN). Osmotolerance and thermotolerance were studied statistically using Response Surface Methodology (RSM) in two selected yeast strains, i.e. S.cerevisiae 11815 and S.cerevisiae D-7 on the basis of OD550, differential microscopic count and plate count. Preconditioned cells of S.cerevisiae 11815 showed optimum temperature and brix of 35oC and 34.686oB with a desirability of 0.748 and preconditioned cells of Saccharomyces cerevisiae D-7 Lalvin having temperature and brix of 35oC and 36.0oB with desirability of 0.743. Maximum ethanol production (12.53%, v/v) was reported with a combination of 35oC and 39oB using preconditioned S. cerevisiae 11815 cells with 17oB of residual brix. Hence fermentation was carried out between (20 to 30oB) of which 24oB was found to be optimum with an ethanol production of 12.4 % (v/v) and 15.3 % (v/v) in S.cerevisiae 11815 and S.cerevisiae D-7. Scale up studies on sugarcane juice at 5L validated the optimized fermentation parameters (Brix 24oB, Inoculum size 7.5% (v/v) and DAHP 0.3% (w/v) leading to 12.4 % (v/v) and 14.7% (v/v) ethanol production with fermentation efficiencies of 80.72% and 95.7% by S.cerevisiae MTCC 11815 and D-7, respectively. Molasses were fermented at 500ml and 5L scale using the preconditioned cells of both yeast strains with specific gravity of 1.190. Alcohol production was found to (10.4 %,v/v) and (10.8%,v/v) in 60 h, respectively. Hence preconditioned cells of both strains revealed higher ethanol production that unconditioned cells.
Self-assembly of the active lactone form of a camptothecin–phospholipid complex for sustained nuclear drug delivery

10-Hydroxycamptothecin (CPT) is considered as one of the most promising anticancer drugs against a broad spectrum of human cancers. However, it is difficult to apply CPT clinically, because of its poor water solubility and reversible instability between the active lactone and inactive carboxylate forms at neutral pH. In this paper, to overcome these limitations, the active lactone form of CPT–soybean phosphatidylcholine (SPC) complex self-assembled nanoparticles (CPT–SPC NPs) is prepared by a co-solvent method combined with a self-assembly technique. The CPT–SPC complex is characterized by solubility, UV-vis, 1H NMR, FTIR, XRD, and fluorescence analysis. These results prove the efficient complexation between active lactone form of CPT and SPC (complexation rate was high as approximately 98%). The self-assembled CPT–SPC NPs show a hydrodynamic particle size of 210.7 ± 6.1 nm, a zeta potential of −24.9 ± 3.1 mV, a spherical shape, and a high drug-loading content of 16.3 ± 0.5%. CPT is released from the CPT–SPC NPs in a biphasic way with an initial burst release followed by a subsequent sustained release. Additionally, in comparision with the free CPT, the CPT–SPC NPs, because of the improved drug stability and enhanced drug transport across cellular membranes, present significantly higher cellular uptake efficiency and cell-killing effect of the drug. Moreover, both confocal imaging and fluorescence measurements demonstrate that CPT is able to be delivered to nuclei by the CPT–SPC NPs after their cellular uptake, by real-time monitoring of drug release and intracellular drug delivery. Furthermore, in vivo animal imaging results indicate that the systemically administered CPT–SPC NPs exhibit excellent tumor targetability in HeLa tumor-bearing nude mice. These results demonstrate that the CPT–SPC complex-based self-assembled NPs hold great potential as effective drug delivery systems for cancer treatment.
Evolution of Australian Cryptocarya (Lauraceae) based on nuclear and plastid phylogenetic trees: evidence of recent landscape-level disjunctions

Abstract. Species-level relationships within the pantropical, largely rainforest genus Cryptocarya R.Br (Lauraceae) and allied groups have long been problematic. Here, we utilise nuclear RPB2 and plastid trnL–trnF sequence data to reconstruct the phylogenetic relationships among Australian Cryptocarya species. We relate our findings to the previous two disparate attempts to resolve species-level relationships on the basis of traditional taxonomic tools. Our results showed that an early diversification gave rise to two lineages present in Australia and globally. The loss of cataphylls (bract-like leaves in seedlings) seems to be a derived state only found in the larger of these two clades. Ruminate cotyledons is another potentially informative character; however, it is highly likely that this condition arose through convergent or parallel evolution. Little or no molecular variation was observed between many species, which suggests recent diversification. Furthermore, the close relationships between species from two geographically disjunct centres of rainforest diversity within Australia suggests that loss of between-region connectivity is recent. A global revision of the group, incorporating molecular analyses and seedling and fruit morphology, is needed to untangle the complex evolutionary relationships within this genus.
Crustacea Amphipoda: Lysianassoids from the tropical western South Pacific Ocean

There are currently 2 0 lys ianassoid amphipod species known from the tropical western South Pac i f i c Ocean. W e report on 32 species from the area, including one new genus (Coriolisa) and 19 new species (Aristias thio, A. uokonia, Bathyamaryllis ouvea, Clepidecrella tropicalis, Coriolisa novacaledonia, Cyphocaris bellona, Hippomedon vao, Kerguelenia koutoumo, K. lifou, Lepidepecreella sarcelle, Onesimoides abyssalis, Socarnes rurutu, S. tiendi, S. tuscarora, Socarnopsis honiara, S. tandai, Trischizostoma richeri, Tryphosella ama and T. oupi). This brings the total species known from the area to 46 .
Interfacial self-assembly of endothelial cells toward angiogenic network formation in the composite hydrogel culture systems

Fabrication of a pre-vascularized tissue in vitro is an extensive research activity. The idea behind this approach is that a network of newly formed micro-vessels may be engineered in vitro by the seeding of a scaffold with endothelial cells. To this aim, understanding the effect of physicochemical properties of the scaffolding material and the method of cell seeding, in regulating endothelial cells’ behavior in the in vitro constructs, is an emerging requirement. In this study, the effect of interfacial self-assembly and contact guidance for the endothelial cell behavior and angiogenic network formation have been studied. This has been done by the fabrication of in vitro three-dimensional tissue constructs, using multilayer surface-modified polymer fibers, and two different methods of cell seeding by human umbilical vein endothelial cells. In the first method, human umbilical vein endothelial cells, fibers, and fibrin gel matrix were combined simultaneously. In the second method, the human umbilical vein endothelial cells and fibers, having various surface coatings, were sandwiched between two layers of fibrin gel matrix with or without fibroblast cell monolayer over the fibrin gel. In the optimal conditions, the effect of fibers in conjunction with the interfacial self-assembly enhanced a tube-like and interconnected network structure formation. This design could therefore have a major impact in the generation of the pre-vascularized tissue-engineered constructs.
Herbicide Detoxification in Plants

Higher plants are equipped with a remarkably versatile system that protects them from the potentially phytotoxic actions of xenobiotics, i.e. synthetic chemicals present in the plant’s environment. Particularly striking is the natural tolerance of certain plants toward herbicides that profoundly affect closely related species. This phenomenon of herbicide selectivity is widely exploited in agriculture to control competing weeds in a field of crop plants that are tolerant to the particular herbicide. Herbicide selectivity is, in most cases, based primarily on the differential ability of plant species to metabolically detoxify the herbicide (Lamoureux et al., 1991; Cole, 1994). Metabolic herbicide inactivation has been employed in the genetic engineering of crops for herbicide tolerance (Hinchee et al., 1993). Finally, enhanced herbicide detoxification is one of the mechanisms of herbicide resistance, in addition to altered target site susceptibility and yet-unknown mechanisms, that may emerge within formerly susceptible weed species upon continuous use of the same herbicide or herbicide class (Holt et al., 1993). It is well documented that plants are able to metabolize and detoxify herbicides by a variety of enzymatic reactions and with extraordinary diversity among species. Furthermore, recent research has revealed that transporters in the vacuolar membrane mediate the energydependent export of herbicide metabolites into the large central vacuole (Martinoia et al., 1993).
Establishment of a DNA-barcode library for the Nemaliales (Rhodophyta) from Canada and France uncovers overlooked diversity in the species Nemalion helminthoides (Velley) Batters

De nombreuses etudes ont montre l'utilite du code a barres ADN pour definir les frontieres des especes d'algues rouges et ont demontre en outre que notre comprehension de la diversite biologique et de la biogeographie des representants de ce groupe etait loin d'etre complete. Nous avons donc constitue des bibliotheques de sequences code-barres ADN des algues rouges canadiennes et francaises. Dans le present article, nous presentons des resultats concernant la diversite de representants des Nemaliales. Quatre-vingt-sept individus des cotes du Canada et de la France ont ete etudies, avec un echantillonnage incluant des specimens provenant de trois oceans (Pacifique, Arctique, Atlantique) et deux mers (la Manche et la Mediterranee). Nos sequences confirment bien la presence et la definition de chacune des 15 especes de Nemaliales que nous nous attendions a recolter dans ces regions, les sequences de leurs representants ayant entre elles des divergences genetiques ≤ 1%, a l'exception de Nemalion helminthoides (Velley) Batters dont il est apparu que les representants etudies constituent cinq lignees differentes, distantes genetiquement entre-elles de 10 a 18 %. Deux specimens de Bretagne et des Asturies ont ete rapportes a Nemalion helminthoides ; nous avons propose provisoirement de nommer nos recoltes du Pacifique Nemalion vermiculare Suringar mais une sequence d'un specimen de la localite type est necessaire pour avoir une certitude ; nous avons ressuscite le nom Nemalion lubricum Duby pour le specimen mediterraneen de ce genre et ressuscite le nom Nemalion multifidum (F. Weber et D. Mohr) Chauvin pour des specimens recoltes des deux cotes de l'ocean Atlantique nord et differant morphologiquement de N. helminthoides. Nous avons aussi decouvert le stade encroutant de Scinaia interrupta (A.P. de Candolle) M.J. Wynne dans les eaux pacifiques canadiennes, ce qui represente une extension significative de la zone de distribution actuellement connue de cette espece. Enfin, nos analyses Bayesiennes du gene nucleaire codant pour l'ARN ribosomique 28S (large subunit ribosomal DNA ou LSU) confirment que Whidbeyella cartilaginea Setchell et N.L. Gardner doit etre place dans les Scinaiaceae ; cette position systematique avait jusqu'ici ete proposee sans certitude, sur la base de l'existence, chez cette espece, de caracteristiques morpho/anatomiques particulieres.
Effects of Neuronal Nitric Oxide Synthase Signaling on Myocyte Contraction during Beta-Adrenergic Stimulation

ii ACKNOWLEDGEMENT . viii VITA . x LIST OF FIGURES . xvii Chapter 1: Introduction . 1 1.1 General Introduction . 1 1.2 Excitation-Contraction Coupling . 2 1.2. 1 Action Potential . 2 1.2. 2 Ca Transient, [Ca]i . 3 1.2. 3 Myocyte Contraction . 5 1.3 Regulation of ECC . 6 1.3. 1 FFR . 7 1.3. 2 The β-adrenergic receptor (β-AR) signaling . 8 1.3. 3 NO signaling . 9 1.3. 4 Role of CaMKII in ECC . 17 1.4 Heart Failure . 19 1.5 NOS signaling in heart failure . 20 1.5. 1 NOS1 signaling in heart failure . 21 1.5. 2 NOS3 signaling in heart failure . 23 xiii 1.5. 3 NOS2 signaling in heart failure . 23 1.6 Specific Aims, Objectives, and Rationales . 24 Chapter 2: CaMKII mediated SR Ca leak is involved in the positive inotropy of NOS1 signaling during β-AR stimulation . 38 2.