Miracle-dz/UniFAR-FTUs huggingface dataset:
Community Level Physiological Profile: a Tool to Assess Functional Microbial Diversity in Soil

Community level physiological profile (CLPP) is a usefull, sensitive and rapid method to assess functional diversity of microbial community as results of measured potential metabolic activity. The use of sole carbon substrate to obtain information about metabolic capacity of soil microflora conducted to the development of different systems which are able to give rapid and sensitive results without excessive costs. The Biolog system and MicroResp system are used most often for CLPP analyses. The paper summarizes work principles, advantages and drawbaks of both methods and highlights the importance of CLPP for soil ecological studies.
How well do we know the Antarctic marine fauna? A preliminary study of macroecological and biogeographical patterns in Southern Ocean gastropod and bivalve molluscs

The aim of this study was to use data for gastropod and bivalve molluscs to determine whether the fauna of the Southern Ocean is sufficiently well known to establish robust biogeographical and macroecological patterns. We chose molluscs for this work because they have been collected by almost every biological expedition to Antarctica, and are relatively well known taxonomically. Sampling of the continental shelf fauna is reasonably full and extensive, although new species are still being described and there are significant gaps in sampling off Wilkes Land and in the Bellingshausen and Amundsen Seas. Species richness was highest in those areas that have been subject to the most intense research activity and this pattern remained even after correction for sampling intensity. The low species richness of the Southern Ocean molluscan fauna compared with many tropical sites is confirmed, and is related principally to the absence of the large number of rare taxa that characterize some tropical assemblages. There is as yet no convincing evidence for a latitudinal cline in molluscan diversity within the Southern Ocean. Multivariate analyses defined biogeographical provinces very similar to those established previously, though they also identified a number of finer‐scale sub‐provinces including a small area of high diversity off Enderby Land. Most Southern Ocean gastropods and bivalves are rare, with limited distributions; relatively few taxa have circumpolar distributions.
Effects of O3 and CO2 on Photosystem II, Nitrate Reductase and Nitrite Reductase in Paddy Rice Leaves

To evaluate the interaction between O3 and CO2 on photosynthesis and nitrogen metabolism in rice, combined exposures of O3 [0, 0.1, 0.3 cm3 m−3 (abbreviated as O0, O0.1, O0.3)] and CO2 [400, 800 cm3 m−3 (abbreviated as C400, C800)] were applied for 5 h using environment-controlled chambers with natural-light. Subsequently, the plants were raised for 3 d under clean air (O0+C400) conditions. Immediately before (BE), immediately after (AE-0), and 1 and 3 d after (AE-1, AE-3) gas exposure, the chlorophyll fluorescence of photosystem II (PSII) and activities of nitrate (NR) and nitrite (NiR) reductase were determined. Results show that maximum (Fv/Fm) and operating (Fq'/Fm') quantum efficiencies and NiR activity were inhibited by O3, but they were ameliorated by elevated CO2, suggesting that the O3-inhibition of photosynthesis accompanied the reduced electron transport toward the downstream of photosystem and suggesting that the reduction power became deficient. Because NiR locates in the chloroplast and uses reducing power from PSII, it must receive a greater O3-inhibition than cytoplasmic NR does.
A new group of plant-specific ATP-dependent DNA ligases identified by protein phylogeny, hydrophobic cluster analysis and 3-dimensional modelling.

The eukaryotic ATP-dependent DNA ligases comprise a group of orthologous proteins that have distinct roles in DNA metabolism. In contrast with the well-known DNA ligases of animal cells, the DNA ligases of plant cells are poorly described. Until now, only two DNA ligases (I and IV) genes of Arabidopsis thaliana (L.) Heynh were isolated and characterised. Use of the complete genomic sequences of Oryza sativa L. and A. thaliana, as well as the partially assembled genomic data of Medicago truncatula L. and Brassica spp. , allowed us to identify a new family of ATP-dependent DNA ligases that are found only in the Viridiplantae kingdom. An in-depth phylogenetic analysis of protein sequences showed that this family composes a distinct clade, which shares a last universal common ancestor with DNA ligases I. In silico sequence studies indicate that these proteins have distinct physico-chemical properties when compared with those of animal and fungal DNA ligases. Moreover, hydrophobic cluster analysis and 3-dimensional modelling allowed us to map two conserved domains within these DNA ligases I-like proteins. Additional data of microsynteny analysis indicate that these DNA ligases I-like genes are linked to the S and SLL2 loci of Brassica spp. and A. thaliana, respectively. Combining the results of all analyses, we propose the creation of the DNA ligases VI (LIG6) family, which is composed by plant-specific DNA ligases.
Enzymatic resolution of (R, S)-Naproxen in water-saturated ionic liquid

A water-saturated ionic liquid has been exploited for resolution of (R, S)-Naproxen by lipase-catalyzed hydrolysis to enhance the conversion and facilitate product recovery. From the enantioselectivity and activity of lipase, water-saturated [bmim]PF6 (1-butyl-3-methylimidazolium hexafluorophosphate) was selected as the best reaction medium. To prevent the dissolution of lipase in the ionic liquid, a weakly polar, amorphous multiporous silica YWG-C6H5 was used as a support for immobilization. The production of (S)-Naproxen was initially performed in a batch reactor containing 20 mL of substrate solution. After 72 h reaction, 98.2% enantiomeric excess of the (S)-Naproxen was obtained with 28.3% hydrolysis conversion. The unconventional solvent properties of ionic liquids have been exploited in reaction medium recycling, product recovery and water recruiting schemes. In a repetitive batch reaction system, the immobilized lipase could be repeatedly used for 5 times with only a slight reduction in reaction conversion.
Viewpoint: How large is the carbon isotope fractionation of the photorespiratory enzyme glycine decarboxylase?

Despite the intense effort developed over the past 10 years to determine the 12C / 13C isotope fractionation associated with photorespiration, much uncertainty remains about the amplitude, and even the sign, of the 12C / 13C isotope fractionation of glycine decarboxylase, the enzyme that produces CO2 during the photorespiratory cycle. In fact, leaf gas-exchange data have repeatedly indicated that CO2 evolved by photorespiration is depleted in 13C compared with the source material, while glycine decarboxylase has mostly favoured 13C in vitro. Here I give theoretical insights on the glycine decarboxylase reaction and show that (i), both photorespiration and glycine decarboxylation must favour the same carbon isotope - the in vitro measurements being probably adulterated by the high sensitivity of the enzyme to assay conditions and the possible reversibility of the reaction in these conditions, and (ii), simplified quantum chemistry considerations as well as comparisons with other pyridoxal 5'-phosphate-dependent decarboxylases indicate that the carbon isotope fractionation favour the 12C isotope by ~20‰, a value that is consistent with the value of the photorespiratory fractionation (f) obtained by gas-exchange experiments.
Strawberry recovers from iron chlorosis after foliar application of a grass‐clipping extract

Bare-root transplants of strawberry (Fragaria × ananassa Duch. cv. Selva) were transferred to nutrient solutions with or without iron. After 35 d of growth, plants in the solution without iron became chlorotic and had morphological changes in roots typical of iron-deficiency chlorosis (IDC). Acidification of the nutrient solution was also observed. We tested a grass-clipping extract to correct IDC in strawberry plants by foliar application to some chlorotic plants. We also assessed the effects of this product on plant growth, Fe allocation, as well as morphological and physiological parameters related with IDC. After the second spray, leaf chlorophyll increased in the youngest expanded leaves. The total content of iron in plants increased from 1.93 mg to 2.37 mg per plant after three sprays, accounting for 80% of the total iron supplied by the extract. Newly formed roots from sprayed plants had a normal morphology (no subapical swollen zone) but a higher ferric chelate–reductase (FC-R; EC 1.16.1.17) activity per root apex compared with roots from plants grown with iron or untreated chlorotic plants. Acidification of the nutrient solution continued in sprayed recovered plants. The results suggest an uncoupling of the regulation of morphological and physiological mechanisms related to IDC: FC-R activity seems to be controlled by roots on their own or together with shoots, while morphological changes in roots are apparently regulated only by the level of iron in shoots.
Longitudinal Analysis of Body Weight and Feed Intake in Selection Lines for Residual Feed Intake in Pigs

A selection experiment for reduced residual feed intake (RFI) in Yorkshire pigs consisted of a line selected for lower RFI (LRFI) and a random control line (CTRL). Longitudinal measurements of daily feed intake (DFI) and body weight (BW) from generation 5 of this experiment were used. The objectives of this study were to evaluate the use of random regression (RR) and nonlinear mixed models to predict DFI and BW for individual pigs, accounting for the substantial missing information that characterizes these data, and to evaluate the effect of selection for RFI on BW and DFI curves. Forty RR models with different-order polynomials of age as fixed and random effects, and with homogeneous or heterogeneous residual variance by month of age, were fitted for both DFI and BW. Based on predicted residual sum of squares (PRESS) and residual diagnostics, the quadratic polynomial RR model was identified to be best, but with heterogeneous residual variance for DFI and homogeneous residual variance for BW. Compared to the simple quadratic and linear regression models for individual pigs, these RR models decreased PRESS by 1% and 2% for DFI and by 42% and 36% for BW on boars and gilts, respectively. Given the same number of random effects as the polynomial RR models, i.e., two for BW and one for DFI, the non-linear Gompertz model predicted better than the polynomial RR models but not as good as higher order polynomial RR models. After five generations of selection for reduced RFI, the LRFI line had a lower population curve for DFI and BW than the CTRL line, especially towards the end of the growth period.
Effects of acidic conditions on the physiology of a green alga (Micractinium sp.) before and after a 5-year interaction with Tetrahymena thermophila in an experimental microcosm

The mechanisms through which algae evolve physiological characteristics related to endosymbiotic associations with heterotrophic organisms remain unclear. We previously showed that a green alga (Micractinium sp.) was able to evolve a host (ciliate)-benefiting phenotype that prolonged the longevity of Tetrahymena thermophila in the absence of bacteria during a 5-year culture period in an experimental microcosm. Comparative experiments between the ancestral alga (i.e. original) and evolved algal clones of the same lineage can be performed to analyse the mechanisms that underlie algal evolution during interactions with ciliates. Here, we investigated the effects of acidic conditions on algal physiology because the acidic conditions within the food vacuoles of Tetrahymena could potentially affect algal evolution during long-term interactions. It might be expected that algal clones isolated from T. thermophila hosts would have developed the ability to resist acidic conditions in order to establish within the host, when compared with the ancestral strain. Unexpectedly, comparative analyses demonstrated that acidic conditions with pH values ranging from 3.9 to 4.3 limited the growth of the isolated algal clones SC9-1 and SC10-2, whereas the ancestral strain could grow under these conditions. Acidic conditions were responsible for significantly lower chlorophyll a/chlorophyll b ratios in the isolated algal clones, and the isolated clone SC9-1 exhibited a high cellular content of chlorophyllide a during a short exposure to acidic conditions, suggesting that degradation of chlorophyll a occurred. Furthermore, acidic conditions increased the release of extracellular glycerol and sucrose in the SC9-1 clone. These results indicated that the ancestral strain showed phenotypic changes related to acidic conditions, which may reflect the ongoing development of an algal phenotype suited to symbiosis. Hypotheses are proposed to explain the limited growth of the isolated clones, and implications for the Micractinium–Tetrahymena association are discussed.
Genetic effects of polymorphisms in the prolactin receptor gene on chicken reproductive traits

Prolactin receptor (PRLR) is a single transmembrane protein through which prolactin plays a wide variety of physiological roles in vertebrates. Markers of alleles for the PRLR gene were assessed for the association with six reproductive traits (bodyweight at first egg; egg weight at first egg; age at first egg; number of eggs at 300 days of age; bodyweight at 300 days of age; and egg weight at 300 days of age) in a single generation of the Erlang Mountain Chicken. Five single-nucleotide polymorphisms were detected in the PRLR gene by sequencing pooled DNA samples. Genotypes were identified using PCR-single strand conformational polymorphism and direct PCR-sequencing methods. The GLM procedure was used to estimate the association between genotypes and reproductive traits. The results showed that at the P1 locus, individuals with genotype TT had shorter age at first egg and greater number of eggs at 300 days of age than those with genotype CC (P G at P1 locus could be a potential genetic marker for age at first egg and number of eggs at 300 days of age in the Erlang Mountain Chicken and haplotype ATGTT might be advantageous for reproductive traits.
Suitability of RAPD analysis for the detection of somaclonal variants in oil palm (Elaeis guineensis Jacq)

Random amplified polymorphic DNA (RAPD) analysis using arbitrary 10-mer oligonucleotide primers was employed in order to investigate the genetic fidelity of somatic embryogenesis-derived regenerants of oil palm (#Elaeis guineensis# Jacq). Clonal palms bearing the "mantled" phenotype were identified in the field and the ability of RAPD markers to distinguish these variants from palms of the normal type was assessed. Of the 387 arbitrary primers used, 259 (67%) were successfully used to amplify oil palm DNA genomic fragments with consistently reproducible banding. Of these 387 primers, 73 (19%) primers enabled the identification of polymorphism between clones. No intraclonal variability and no differences between mother palms and regenerants could be identified using the total number of markers scored (8900). Twenty-four of these 73 primers were chosen for use in a larger experiment aimed at comparing, first, the mother palm genome with that of its clonal offspring and, second, true-to-type and variant regenerants. Thus, the regeneration protocol based on somatic embryogenesis set up for oil palm clonal propagation does not induce any gross genetic changes. The results obtained revealed however, that the RAPD approach is not suitable for the detection of the "mantled" variant phenotype. The use of RAPD markers for the detection of somaclonal variation in oil palm is discussed. (Resume d'auteur)
N, P Contribution and soil adaptability of four arbuscular mycorrhizal fungi

Abstract A glasshouse study was conducted to investigate the symbiotic efficiency and soil adaptability of four AMF using glass-bead cultivation systems. The results showed that efficiency and adaptability of four fungi varied among three soils. Particularly, efficiency of BEG167 shifted from positive in Beijing soil to negative in Guangdong soil. Furthermore, BEG167 had high adaptability in all three soils. Intraspecific differences of BRG168 and BEG221 were found in efficiency and adaptability in three soils. Taking efficiency and adaptabilty into consideration, it was concluded that BEG167, BEG168 and BEG221 in Beijing soil, BEG151 in Hubei soil, and BEG151 and BEG168 in Guangdong soil were effective AMF for maize.
Development of new polymorphic microsatellite markers for the New World screw-worm Cochliomyia hominivorax (Diptera: Calliphoridae)

In this report, we describe the development of seven new polymorphic microsatellite markers for Cochliomyia hominivorax , a parasitic insect pest of primary agricultural and veterinary importance throughout the Neotropics. The number of alleles found ranged from 3 to 13 per locus, with the expected heterozygosity ranging from 0.4220 to 0.9045. The across-taxa amplification of some of these new microsatellite loci was successful in four additional Calliphoridae species. In combination with the 10 polymorphic microsatellite markers previously described, the markers developed here should provide a high resolution for assessing the fine-scale genetic structure of New World screw-worms.
Induction of Macrophage-Inflammatory Protein-3α Gene Expression by TNF-Dependent NF-κB Activation1

Macrophage-inflammatory protein-3α (MIP-3α), also designated as liver and activation-regulated chemokine (LARC), Exodus, or CCL20, is a recently identified CC chemokine that is expected to play a crucial role in the initiation of immune responses. In this study, we describe that MIP-3α expression is under the direct control of NF-κB, a key transcription factor of immune and inflammatory responses. Overexpression of the p65/RelA subunit of NF-κB significantly increased the MIP-3α mRNA level. MIP-3α transcription was stimulated by TNF, and this stimulation was inhibited by an NF-κB inhibitor, I-κBα superrepressor. Analysis of the human MIP-3α promoter demonstrated a functional NF-κB site responsible for its expression. We also show that MIP-3α expression is induced in LPS-treated mouse livers that were primed with Propionibacterium acnes, which developed massive liver injury with infiltration of inflammatory cells. This induction was fully dependent on the TNF signaling cascade, because it was not observed in the livers of TNFR1-deficient mice. Furthermore, pretreatment with gliotoxin, an inhibitor of NF-κB activity, abrogated the P. acnes/LPS-induced MIP-3α expression of wild-type mice. These results clearly demonstrate that MIP-3α gene expression is dependent on NF-κB activity in vitro, and indicate that the TNFR1-mediated TNF signaling cascade that leads to NF-κB activation plays an essential role in MIP-3α expression in the murine liver injury model.
Pollination Success and Reproductive Output in Experimental Populations of the Self‐Incompatible Primula vulgaris

We studied the effects of population size, plant density, and interpopulation distance on the process of sexual reproduction in experimental populations of the perennial self‐incompatible Primula vulgaris (Primulaceae). Decreasing population size significantly reduced the proportion of flowers setting fruit, the seed:ovule ratio, and the overall seed production per plant, whereas no density effect was observed for any of the measured reproductive components. The seed:ovule ratio decreased more strongly and significantly with decreasing population size when populations were more spatially isolated. Increasing interpopulation distance also significantly reduced seed production per fruit and per plant. We found indications that skewed morph frequencies, associated with population size, may further reduce reproductive success as supplemental hand pollinations revealed that a lack of compatible pollen significantly reduced fruit and seed production, especially in individuals belonging to the morph in majority. Although the effects of morph bias and population size could not be investigated separately, we conclude that reproductive success in small populations of P. vulgaris is significantly affected by combined effects of reduced pollinator services and limited availability of compatible morphs (deficit in compatible pollen). As such, this study exemplifies the importance of a plant breeding system in determining reproductive success in fragmented populations of self‐incompatible species.
Cross-utility of microsatellite markers across species of the African Poicephalus parrots to encourage conservation research

The genus Poicephalus is one of four genera of parrots found on the African continent. However, little is known about this group of parrots as few studies have been undertaken in the wild and they remain one of the least studied groups of parrots. Decisions on their conservation status and determining appropriate trade quotas are often based on very limited information. Observing and collecting ecological and behavioural data on parrots in their natural habitat is difficult and accordingly the data from wild populations are limited. Genetic markers provide a potential method to obtain data on a species’ ecology, e.g. effective population size and reproductive behaviour, which can assist conservation management. However, developing or screening genetic markers for such investigations can be costly and time consuming and is not guaranteed; these constraints may deter researchers from considering or including them in proposals. This study has characterised 17 microsatellite loci across most species of the African Poicephalus parrots in order to encourage researchers to collect samples and/or to develop genetic studies for Poicephalus parrots. Additional knowledge from wild populations will benefit these little-known parrots.
Amylose and Amylopectin Interact in Retrogradation of Dispersed High-Amylose Starches

ABSTRACT Retrogradation of three high-amylose starches (HAS: ae du, ae V, and ae VII) and common corn starch (CCS) was examined by dynamic oscillatory rheometry (7.5% [w/w] starch in 20% [v/v] dimethyl sulfoxide [DMSO]), differential scanning calorimetry (DSC; 30% [w/w] starch in water), and turbidity (0.5% [w/w] starch in 20% [v/v] DMSO). Nongranular lipid-free starch and starch fractions (amylose [AM], amylopectin [AP], and intermediate material [IM]) were studied. Gels were prepared by dispersing starches or fractions in 90% DMSO and diluting with water, followed by storage for seven days at 4°C. For AM from each starch, the elastic modulus (G′) was similar when heated from 6 to 70°C. The G′ of HAS AP gels at 6°C was higher than for CCS AP gels. For nongranular CCS and ae du gels, G′ dropped dramatically (≈100×) when heated from 6 to 70°C, less (≈10×) for ae V gels, and least (≈5×) for ae VII gels. By DSC, each AM endotherm had a peak temperature of ≈140°C, whereas all AP endotherms were complete befor.