Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative study of heme and Mg-protoporphyrin (monomethyl ester) biosynthesis in isolated pea chloroplasts : Effects of ATP and metal ions

The flux of porphyrins through the iron and Mg-chelatase reactions in pea (Pisum sativum L., cv. spring) chloroplasts was estimated. The chloroplasts were administered exogenous δ-aminolevulinic acid (ALA) and heme synthesis was quantitated by incorporation of [ 14 C]ALA. Flux through Mg-chelatase was estimated by measuring levels of the first committed intermediates in the pathway, Mg-protoporphyrin-IX and its monomethyl ester [Mg-Proto(Me)]. In the presence of ATP, four major effects were noticeable: (a) Mg-Proto(Me) accumulation was ten-fold greater than heme accumulation; (b) Heme synthesis was suppressed by 68%; (c) Mg-Proto(Me) accumulated, and no Proto was detectable; (d) The total amount of Mg-Proto(Me) plus heme was 80% higher than the protoporphyrin + heme content in the absence of ATP. The accumulation of protoporphyrin from ALA could be increased 30% by incubation with ATPγS; under these conditions no Mg-Proto(Me) accumulated. The presence of Fe 2+ stimulated Mg-Proto synthesis from both ALA and porphobilinogen substrates. This stimulation was observed at 0.1 mM ALA, but not at 1 mM ALA. Iron also stimulated the uptake of ALA into the chloroplasts; the time course of ALA uptake in the presence of Fe 2+ resembled that for Mg-Proto(Me) synthesis at 0.1 mM ALA in the presence of Fe 2+ .
Using Visual Feature Space as a Pivot Across Languages

Our work aims to leverage visual feature space to pass information across languages. We show that models trained to generate textual captions in more than one language conditioned on an input image can leverage their jointly trained feature space during inference to pivot across languages. We particularly demonstrate improved quality on a caption generated from an input image, by leveraging a caption in a second language. More importantly, we demonstrate that even without conditioning on any visual input, the model demonstrates to have learned implicitly to perform to some extent machine translation from one language to another in their shared visual feature space. We show results in German-English, and Japanese-English language pairs that pave the way for using the visual world to learn a common representation for language.
Realistic simulation of the effects of abundance distribution and spatial heterogeneity on non-parametric estimators of species richness

Abstract: Several non-parametric estimators have been proposed for estimating species richness from a spatial sample. While the label non-parametric may suggest that a method makes few assumptions, these estimators are known to rely on a homogeneous community with certain abundance distributions. In this paper we simulate the effect of different abundance distributions (geometric series, log-normal, and broken-stick models) and of different types of spatial heterogeneity (species-specific aggregation, gradients, and an edge effect) on the performance of four non-parametric estimators of species richness for presence-absence data (Jack1, Jack2, Chao2, and ICE). In order to focus on parameter settings likely to be encountered in real communities, we derived simulation parameters from real data from four agricultural habitat types in central Switzerland. Based on an ANOVA of relative bias, all estimators failed for communities simulated under the geometric model and were considerably affected by a simulated edge effect, but species-specific aggregation, an environmental gradient, and differences between community types had little effect on estimator performance. Species abundance distribution and spatial heterogeneity influence estimator performance by decreasing the proportion of species represented in the sample, which may be counteracted by adapting the sampling design. For reasonably complete samples, Chao2 was the least biased, but suffered from a large variance, as did Jack2. We recommend using the first order jackknife Jack1 or the incidence-based coverage estimator ICE, but only for samples that contain at least 80% of the species.
Diet, size and location as determinants of n‐3 long‐chain polyunsaturated fatty acid content in farmed Atlantic Salmon (Salmo salar)

We explored how currently manufactured feeds, under real-world conditions and across geographically distinct locations, promoted flesh n-3 long-chain polyunsaturated fatty acid (LC-PUFA, i.e. 20:5n-3 + 22:6n-3) levels in various life stages of farmed Atlantic Salmon (Salmo salar). Potential effects on flesh LC-PUFA included: (1) diet and fish weight at one Canadian east coast farm, (2) diet and farm location across six east coast farms, and (3) diet and farm location between east and west coast farms. For objectives 1 and 2, salmon were fed a currently manufactured feed (labelled as feeds A, B or C) and harvested at 1, 3 and 5 kg. LC-PUFA levels in 5 kg (harvest size) fish were then compared to previously published values for west coast farmed Atlantic Salmon (Obj. 3). Combined results revealed that variability in LC-PUFA levels was better explained by diet than by fish weight or farm location. Fish size, however, was also important for two reasons. First, feeding a high LC-PUFA diet early in life appeared important for ensuring high LC-PUFA levels at harvest size. Second, salmon flesh LC-PUFA levels increased with fish size, but only when dietary LC-PUFA was provided above an apparent threshold value (~3000 mg per 100 g or 10% of total fatty acids) that likely promoted LC-PUFA incorporation and storage. Overall, our comparison makes new recommendations for feed manufacturers and demonstrates that farmed Atlantic Salmon reared under real-world conditions on currently available salmon feeds were good sources of n-3 LC-PUFA to consumers.
Cross-Resistance of Imazethapyr-Resistant Common Sunflower (Helianthus annuus) to Selected Imidazolinone, Sulfonylurea, and Triazolopyrimidine Herbicides

The study was conducted to determine the cross-resistance of imazethapyr-resistant common sunflower (Helianthus annuus) to selected imidazolinone, sulfonylurea, and triazolopyrimidine herbicides. Whole-plant herbicide dose–response curves and in vitro enzyme studies showed that imazethapyr-resistant common sunflower was highly resistant to imazamox, slightly resistant to thifensulfuron and chlorimuron, and not resistant to cloransulam. Resistance ratios of herbicide concentrations required to inhibit growth by 25% were 310, 3.3, 2.0, and 1.4 times greater in the resistant biotype than in the susceptible biotype for imazamox, thifensulfuron, chlorimuron, and cloransulam, respectively. Similarly, herbicide concentrations required to inhibit ALS activity in vitro by 25% were 332.0, 18.6, 8.3, and 1.2 times greater in the resistant biotype than in the sensitive biotype for imazamox, chlorimuron, thifensulfuron, and cloransulam, respectively.
Schistosoma mansoni sirtuins : characterization of their role in schistosome energy metabolism

This thesis focuses on the metabolism of the parasite Schistosoma mansoni. During its life cycle, S. mansoni experiences drastic environmental changes that include: free-living stages in water and endoparasitism in invertebrate (i.e. snails) and vertebrate (i.e. mammals) hosts. In consequence, this parasite shows an amazing metabolic plasticity characterized by drastic metabolic switches from one stage to another. One of the more interesting is the switch from oxidative phosphorylation to aerobic glycolysis that occurs when the free-living stage, cercariae, infects the mammalian host. This switch is dependent on host glucose and is totally reversible when glucose concentration is low. Here, we study in details the evolution of the glucose transporters of S. mansoni as well as the potential role of histone modifying enzymes (i.e. sirtuins) in the regulation of the metabolic switch. The thesis is organized of three chapters. Chapter I is a general introduction to genus schistosoma, its taxonomy and more prominent members, their epidemiology and current control strategies. We further introduce our current knowledge on the epigenetic machinery of these parasites as well as the sirtuin protein family. In Chapter II we present the results of the thesis and this chapter is separated in two parts: (i) the evolution and molecular properties of glucose transporters in S. mansoni, (ii) and the role of Sirtuin 1 in the regulation of the mitochondrial metabolism of schistosomula, the mammalian stage of S. mansoni. We found that the glucose transporters from S. mansoni, SGTP1, SGTP2, SGTP3 and SGTP4 followed different evolutionary paths. Our results suggested that S. mansoni class I glucose transporters (SGTP2 and SGTP3) lost their capacity to transport glucose and that this function evolved independently in the Platyhelminthes-specific glucose transporters (SGTP1 and SGTP4). Regarding the role of sirtuins in the regulation of glucose metabolism in S. mansoni, we found that at high concentrations of glucose, S. mansoni sirtuin 1 (SmSirt1) stimulate mitochondrial activity. Sirtuin 1 Inhibitors as well as SmSirt1 gene knockdown, by RNA interference, reduce the mitochondrial activity of schistosomula. In addition, SmSirt1 is a repressor of pyruvate dehydrogenase kinase 1 (PDK1), a major regulator of mitochondrial activity. However, SmSirt1 did not appear to repress the S. mansoni glucose transporters. This is in agreement with our analysis of glucose transporter evolution because in mammals, Sirt1 regulates the expression of class I glucose transporters and our results showed that class I glucose transporters in S. mansoni do not transport glucose. Finally, in Chapter III we make a general discussion of the main findings of the thesis.
A molecular and morphological phylogeny of the extant Augochlorini (Hymenoptera, Apoidea) with comments on implications for biogeography

The Augochlorini Beebe is a New World tribe of bees comprising 663 described species. Relationships among the genera of this monophyletic tribe remain uncertain. Here I provide a comprehensive phylogeny using morphological and molecular information. In all, 54 Augochlorini species plus 16 outgroups and 3017 molecular and 105 morphological characters were analysed. Sequences for four genes were analysed using Bayesian inference, maximum likelihood and parsimony. Morphological characters were taken from a literature review and analysed alone and in combination with molecular data using parsimony. The monophyly of Augochlorini and most genera is confirmed, with divergence of the main lineages of the tribe around 55–20 Ma. Seven clades were supported by most analyses and are here treated as genus‐level groups, as follows (combined analysis topology): (Corynura group, (Chlerogella group, (Rhinocorynura group, (Augochloropsis, (Megaloptidia group, (Neocorynura group, (Augochlora group, Megalopta group))))))). According to this topology, dim‐light foraging and cleptoparasitism arose three times in the tribe. According to my hypothesis, the diversification of Augochlorini may have begun as a response to vicariant events, including the split of the Neotropical/Andean regions and marine transgressions in the Amazon region.
New case of fruit eating observation in Podarcis siculus (Rafinesque-Schmaltz, 1810) (Lacertidae) from Croatia

The switch to frugivory in some members of the family Lacertidae is expected to be adaptations for island life, where commonly used prey sources are limited. Herein we reported upon our observation a new case of frugivory in Podarcis siculus from Istria, Croatia. During several excursions to Veruda Island near Pula we repeatedly photographed and observed feeding of these lizards on fruit remains and fresh fruits. Lizards tried to nibble and lick juice or took and swallow fleshy pieces from the fruits. The behavior was independent on season and was observed at both the rocky coast with a sparse vegetation cover as well as in grassy habitats in the center of the island.
Phylogenetic position and systematics of the bryozoan Tennysonia : further evidence for convergence and plasticity in skeletal morphology among cyclostome bryozoans

Cyclostomes are an ancient order of marine bryozoans with a fossil record extending back over 450 million years into the Ordovician. The current taxonomy of both fossil and modern cyclostomes is based almost entirely on skeletal characters but newly available sequence data are beginning to reveal rampant convergence of some of them. An unusual combination of skeletal characters in the South African cyclostome Tennysonia stellata Busk, 1867 has made this genus difficult to classify. After revising the taxonomy of Tennysonia, we use almost complete small and large ribosomal subunits (ssrDNA and lsrDNA) to demonstrate its close phylogenetic affinity with the tubuliporine genus Idmidronea (family Tubuliporidae) with which it shares a similar colony form, despite the presence of skeletally open kenozooids between the autozooids, reminiscent of cerioporine cyclostomes such as Favosipora. The spaces between the transverse rows of autozooidal apertures, occupied by exterior autozooidal frontal walls in Idmidronea, are occupied by kenozooids in Tennysonia, thereby maintaining the spacing between lophophores necessary for efficient suspension feeding. Sympatric colonies of T. stellata with narrow and broad branches are identical or almost identical on the basis of ssrDNA and lsrDNA sequences, respectively, suggesting within-species ecophenotypic plasticity in this aspect of colony form.
Site fidelity, residency, and abundance of bottlenose dolphins (Tursiops sp.) in Adelaide's coastal waters, South Australia

Little is known about the ecology and behavior of southern Australian bottlenose dolphins (Tursiops sp.). This hinders assessment of their conservation status and informed decision-making concerning their management. We used boat-based surveys and photo-identification data to investigate site fidelity, residency patterns, and the abundance of southern Australian bottlenose dolphins in Adelaide's coastal waters. Sighting rates and site fidelity varied amongst individuals, and agglomerative hierarchical cluster analysis led to the categorization of individuals into one of three groups: occasional visitors, seasonal residents, or year-round residents. Lagged identification rates indicated that these dolphins used the study area regularly from year to year following a model of emigration and reimmigration. Abundance estimates obtained from multisample closed capture-recapture models ranged from 95 individuals (SE ± 45.20) in winter 2013 to 239 (SE ± 54.91) in summer 2014. The varying levels of site fidelity and residency, and the relatively high number of dolphins found throughout the study area highlights the Adelaide metropolitan coast as an important habitat for bottlenose dolphins. As these dolphins also appear to spend considerable time outside the study area, future research, conservation, and management efforts on this population must take into account anthropogenic activities within Adelaide's coastal waters and their adjacencies.
Cell Cytoplasm Compartmentalization: Localization Through Gradients

During embryonic development, precursor germ cells contain aggregates of protein and RNA known as germ granules. These germ granules are important in the specification of a functioning germ line, i.e. functioning sex cells within mature organisms. In the single cell fertilized embryo of the nematode worm C.elegans, germ granules (referred to as P granules) localize to the posterior side of the cell. After cell division occurs, they are found only in the posterior daughter cell. The localization behavior of P granules has been a topic of much interest, and considered an important aspect of symmetry breaking during development. We learn the fundamental properties of P granule localization, and determine possible parameters and features of this biological system by developing theory in close collaboration with experimental evidence. In this study, experimental evidence is presented which shows that P granules are liquid droplets, and that their localization occurs through preferential nucleation and growth behavior on one side of the cell and simultaneous preferential dissolution on the opposite side. It is also shown that this behavior is linked to the concentration gradient of the protein Mex-5 along the anterio-posterior axis of the cell, which is necessary to induce the preferential growth of P granules. From this experimental data, a theoretical model for the preferential growth of P granules is developed, where the localization of P granules occurs by phase separation. That is, P granules separate from the bulk cytoplasm by a process described by a first order liquid-liquid phase transitition, where a liquid droplet granule phase nucleates and then grows out of the bulk liquid cytoplasmic phase. In this model, a spatial gradient is imposed on the saturation point, the boundary point between the single phase state consisting only of the cytoplasm, and a metastable state which includes both a P granule and cytoplasm phase. This gradient mimics the properties of the Mex-5 gradient and is sufficient in explaining P granule localization. Using numerical simulations, the theoretical model is studied. It is found sufficient to both successfully describe P granule localizaion, and to describe interesting behavior in a system with assymetric growth due to a spatial gradient. From a purely theoretical standpoint, we observe cyclical non-equilibrium steady states, where material is cycled back and forth along the gradient. From the biological side, experimental properties of the system, such as the diffusion coefficient of P granules and P granule growth rates are determined through both simulation and image analysis of data. In addition, the possiblility of different types of growth behavior at later cell stages, and a method of long range intracellular signalling are suggested from the theoretical model.
The evolution of cavitation resistance in conifers

Forests worldwide are at increased risk of widespread mortality due to intense drought under current and future climate change. In particular, conifer species seem extremely vulnerable to mortality due to hydraulic failure or embolism. The main objective of this thesis was to examine conifer resistance to embolism in an evolutionary framework. Firstly, we uncovered 9-fold variation in resistance to embolism across 250 species from the 7 conifer families, culminating in a new world record in Callitris tuberculata (P50 = -18.8 MPa). We demonstrated the evolutionary relationship between increased embolism resistance and the anatomy of bordered pits. By combining this unprecedented physiological dataset with a time-calibrated phylogeny of over 300 species, we retraced conifer diversification and the evolution of embolism resistance. We discovered multiple evolutionary dynamics with several conifer lineages shifting to higher rates of speciation and trait evolution. We found that conifers with high drought resistance diversified more rapidly, especially crown groups of Cupressaceae composed of the Cupressus-Juniperus clade and the Callitris clade. Within this last group, diversification rates increased over the course of the aridification of Australia over the last 30 million years. We show how their xylem has been shaped by drought, becoming more resistant to embolism, but crucially we found no trade-off with water transport efficiency or construction costs. This work greatly expands our understanding of how vascular plants have evolved to cope with extreme drought.
Study of Chemical Composition and Efficacy of Different Extracts of Iranian Propolis on the Microbiological and Sensory Parameters of Minced Cyprinus carpio Meat at 4°C Storage

ABSTRACT This study has evaluated the effects of different concentrations of the water and ethanolic extracts of Iranian propolis (WEP and EEP) on the microbiological and sensory parameters of minced common carp meat that was stored at 4°C for 9 days. The chemical compounds of the extracts were identified by gas chromatography–mass spectroscopy (GC-MS) analysis. The results revealed that WEP and EEP extracts were efficient against the spoilage microorganisms, including total plate counts (TPCs), psychrotrophic populations (PTCs), lactic acid bacteria (LAB), and even Staphylococcus aureus. There was a significant difference in the bacteria growth between samples treated with WEP or EEP and the control sample during storage. Inhibitory effects were, respectively, 7% EEP > 5% EEP > 3% EEP > 7% WEP > 5% WEP > 3% WEP. In all treatments, PTC counts were higher than 7 log CFU/g after 6 days as well as TPC, LAB, and S. aureus populations after 9 days. Overall, the results show that EEP and WEP have good antimicrobial activity due to high phenolic and flavonoid compounds, including caffeic acid, tectochrysin, aceacetin, chrysin, pinostrobin, pinobanksin-3-acetate, galangin-3-methyl ester, and pinocembrin chalcone. Sensory evaluation shows very slight improvement in sensory properties (color, odor, texture, and overall acceptability) of the treated samples with the different extracts of Iranian propolis.
Genome-wide association study of dynamic developmental plant height in soybean

Abstract: Plant height (PH) is an important agronomic trait affecting crop yield and quality. In this study, a soybean collection of 192 natural accessions and 1536 single nucleotide polymorphism (SNP) makers were used to identify genomic regions associated with PH. There is a large genetic variation in PH with a diverse panel. Three phenotypic indexes (PH measured at six stages, the conditional PH, and the relative growth rates of PH) were used to identify developmental behavior for PH in soybean. Six methods were used to minimize false-positive associations in association mapping, and finally the generalized linear model for principal component analysis had been used in this study. Three SNPs, BARC-040651-07807, BARC-030433-06867, and BARC-042475-08274, were highly significantly associated with PH in the final growing period, and two SNPs, BARC-038795-07333 and BARC-013749-01246, were connected with PH in the early growing period.
Evaluation on Phytochemical Constituents and Antioxidant Activities of Various Formula from Ko-Klan Remedies by Aqueous Infusion Preparation Method

Ko-Klan remedy is Thai folklore medicine appear on list of Thai herbal medicinal products which have been widely used to relief of muscle pain. The remedy were separated to 3 recipes; first, Mallotus repandus: Rhinacanthus nasutus: Elephantopus scaber: Aegle marmelos ; 1: 1:1:1 (w:w:w:w), second, Mallotus repandus: Rhinacanthus nasutus: Elephantopus scaber: Aegle marmelos; 5:2.5:1.5:1.5 (w:w:w:w), third, Mallotus repandus: Rhinacanthus nasutus: Elephantopus scabe: Ceasalpinia sappan: Cryptolepis buchanani: Piper interruptum; 2:1:1:2:2:2 (w:w:w:w). Aims of this study were evaluated to total phenolic (TPC) and flavonoids (TFC) content, and antioxidant activities of various formulas from KoKlan remedy extracts by water infusion preparation. The TPC and TFC were determined to chemical composition. The antioxidations were tested using by 2,2-diphenyl-1-picrylhydrazy (DPPH) radical scavenging, and 2,2 -azinobis-(3-ethylbenzothiazoline-6-sulphonate) (ABTS) assay. The results showed that, the 1 remedy were higher contents of TPC and TFC (12.7927±0.0762 mgQE/gExt and 40.7925± 0.5372 mgGE/gExt), the 2 remedy was highest antioxidant activity by ABTS assay (IC50 = 0.0022± 0.00002 mg/mL), the 3 remedy were highest free radical scavenging by DPPH assay (IC50 = 0.0122± 0.00005 mg/mL). The finding studies suggest that all of the remedy were antioxidation higher than Ascorbic acid and Trolox as standard substances. Further study, some chemical compound(s) and pharmaceutical activity were clarified to medicinal plant use on health promotion.