Miracle-dz/UniFAR-FTUs huggingface dataset:
Grapevine ( Vitis vinifera L.) promoter analysis by biolistic-mediated transient transformation of cell suspensions

Expression of alcohol dehydrogenase promoters from Vitis vinifera L. and Arabidopsis thaliana was investigated in homologous and heterologous cell systems after bombardment of chimeric genes. The effect of several parameters including wounding, DNA delivery and construct type on luciferase/beta-glucuronidase activities was evaluated. In parallel, alcohol dehydrogenase activity was assayed in normal and gaseous nitrogen-treated cells. Compared to A. thaliana , results showed large differences in reporter gene activity according to the Adh promoter leader sequence and the cell suspension system. The V. vinifera cell system was found to be appropriate to investigate Adh promoter functioning. A novel protocol, based on transient genetic transformation of grape-One cells by biolistic is proposed to study grapevine promoter expression, either in air or in response to anaerobiosis.
Assessing reproductive status in orang‐utans by using urinary estrone

The aim of this work was to compare normal menstrual cycle patterns of urinary estrone excretion in orang-utans with those of an orang-utan in her late 40s, an orang-utan before and after rehabilitation for anorexia, and an orang-utan during prolonged lactation. A detailed menstrual and sexual activity record was kept for each orang-utan subject. Urine samples for estrone radioimmunoassay were collected daily for two cycles whenever possible. “Mawas,” in her late 40s, was monitored for two cycles in each of 3 successive years. While the normal pattern of estrone excretion was initially seen, some of the later cycles were shorter and appeared to lack the large luteal-phase peak. “Puspa,” anorexic and amenorrhoeic at the age of 9½ years, had very low urinary estrone concentrations. After rehabilitation, followed by a late menarche, she had regular menstrual cycles with a normal estrone excretion pattern. She gave birth to a normal infant in 1990. “Puteri,” who had been lactating for 2 years, had consistently low estrone concentrations during an 8-week monitoring period, with no evidence of cyclic variation in estrone excretion. Daily urinary estrone measurements, together with observation, were found to be useful in assessing the reproductive status of orangutans.
Presence of several cellulose-binding proteins in cell lysate of Fibrobacter succinogenes S85

Attempts were made to analyze the substances involved in the adhesion of cells of F. succinogenes S85 to cellulose. Firstly, the effect of the treatment of the cells with enzymes on their adhering ability to cellulose was examined. Treatment of cells with proteolytic enzymes such as proteinase K, thermolysin, protease Type IV and trypsin, and with lipase reduced markedly their adhering ability to cellulose, whereas their adhering ability to cellulose was not affected by treatment with acid phosphatase, DNase 1, RNase A and RNase T1. These results show that some proteins on the cell surface are involved in the adhesion of cells to cellulose. Next, attempts were made to detect some of the proteins capable of adhering to cellulose in cell lysate of the bacterium. After Avicel cellulose was incubated in the cell lysate of the bacterium at 37°C, cellulose was washed several times with buffer containing Softes 12 as a detergent to remove the cell debris and proteins incapable of adhering to cellulose. Proteins strongly adhering to cellulose after washing were eluted with buffers containing 1% carboxymethylcellulose (CMC) or 10% cellobiose. When the proteins eluted with CMC were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), one major band and many minor bands were detected in the gel. When the proteins eluted with cellobiose were analyzed by SDS-PAGE, one major band, one minor band and two faint bands were detected in the gel. The major protein in both eluents using CMC or cellobiose, exhibited the same molecular weight of approximately 120 kilodaltons (kDa). These CBPs in cells of the bacterium disappeared after treatment with proteinase K, whereas these CBPs in cells remained after treatment with lipase.
DNA Barcoding of Red Jungle Fowls (Gallus gallus philipensis Hatchisuka) from Different Mountain Areas in the Philippines

Initially proposed as a global standard for rapid species identification, DNA barcodes (cytochrome c oxidase subunit I or COI in the mitochondrial genome) were determined to assess diversity and genetic distances among 25 red jungle fowls (Gallus gallus philipensis Hatchisuka) obtained from different mountain areas in 23 provinces of 12 islands in the Philippines. Results of the evolutionary analyses using Kimura two-parameter model in MEGA5 indicated existence of two main evolutionary clades, and effectiveness of DNA barcodes in identifying and differentiatiang red jungle fowls between and within clades. Genbank-accessed COI sequences of three subspecies of red jungle fowls (Gallus gallus gallus, Gallus gallus bankiva, Gallus gallus spadiceus) and three Gallus species (G. lafayettei, G. sonneratii, G. varius) were clustered in the intermediate zone between differentiated populations of Philippine red jungle fowls, but more recently diverged with those in Clade A. Based on 627 positions from 25 COI sequences, average genetic distance among red jungle fowls was 0.254 units, demonstrating close resemblance within clade, but greater divergence between clades (d>1). Genetic divergence within Clade A (d=0.294) was higher than Clade B (d=0.215). Moreover, pooled pair-wise genetic distance was not significantly correlated (P>0.05) with geographical distances among red jungle fowls between and within clades. Evolutionary analysis of the DNA barcodes of Philippine red jungle fowls provided important information on genetic variability and population structure useful to support decisions on agrobiodiversity conservation and research in upland areas.
Black spruce trees from fire-origin stands have higher wood mechanical properties than those from older, irregular stands1

In the eastern Canadian boreal forest, long fire return intervals lead to over 60% of stands having an irregular, uneven-aged structure, which is associated with slower growth. The aim of this study was to examine the effect of stand structure on the clear wood mechanical properties of black spruce (Picea mariana (Mill.) B.S.P.). A total of 128 trees were destructively sampled from stands of regular and irregular structure across Quebec, Canada. Nonlinear mixed-effects models were developed for each stand type to describe the variation in modulus of elasticity (MOE) and modulus of rupture (MOR) in small defect-free samples as functions of cambial age and annual ring width. Mechanical properties were strongly related to cambial age, with a smaller influence of ring width. After accounting for these variables, both MOE and MOR were higher in samples from stands of regular structure, although differences were less pronounced in the upper stem compared with breast height. The fixed effects of the models expla.
Molecular and embryonic evidence of apomixis in cassava interspecific hybrids (Manihot spp.)

In cassava, apomixis could fix hetereozygosity and prevent the transmission of systemic pathogens which complicate vegetative propagation of the crop. Evidence from maternal inheritance of RAPD markers and the structure of the embryonic sac in large progeny sets of two distinct genotypes have further confirmed that apomixis occurs in cassava. Here, we have built on an earlier report of apomixis in cassava in four ways (1) we estimated the rate of faculative apomixis in the range of 2% (2) we detected the occurrence of apomixis in a second genotype, derived form a different interspecific cross; (3) apomictic behavior was demonstrated in an F1 individual and (4) embryonic evidence showed that the mode of apomixis is aposporic. Since apomixis was detected in an F1 interspecific hybrid it is possible that genes for apomixis could be transferred directly to cultivated cassava from a wild relative. Key words: Cassava, interspecific hybrid
State of preservation of polymorphic plasma proteins recovered from ancient human bones

Protected by the mineral matrix, bone proteins are capable of surviving inhumation periods of several hundreds or thousands of years in soil. While the preservation of the bone matrix protein, collagen I, is the prerequisite for a variety of archaeometric approaches, such as radiocarbon dating and the reconstruction of palaeodiet by stable isotope analysis, little is known about both the rate and state of preservation of non-collagenous proteins. We succeeded in the isolation, electrophoretic separation (SDS-PAGE, IEF) and immunological detection (radial immunodiffusion, IEF immunoblotting and ELISA) of plasma proteins preserved in archaeological human bones. However, sample preparation and electrophoretic methods had to be adapted to the specific demands of these aged proteins, since they are not only degraded and fragmented but also cross-linked to other organic components, either indigenous to the bone or to contaminants from the burial environment. Complex decomposition phenomena are responsible for the altered mode of migration of aged proteins through a gel. After isoelectric focusing, the ancient proteins mainly concentrate below pH 4.45 in the pH-gradient. Thus, highly negatively charged protein components have a better chance of preservation in bone after death. Isoelectric focusing with subsequent immunoblotting of ancient protein samples revealed protein patterns which showed marked charge-modifications in comparison with those of modern human plasma proteins due to protein degradation (e.g. α2-HS-glycoprotein and α1-antitrypsin). Nevertheless, in combination with different immunological analyses, previous results concerning the selective enrichment of α2-HS-glycoprotein in bone compared with other plasma glycoproteins could be confirmed. Copyright © 1999 John Wiley & Sons, Ltd.
220 AN EXPRESSION PROFILE OF GENES CRUCIAL FOR PLACENTAL DEVELOPMENT IN SINGLE IN VIVO, IN VITRO AND CLONED BOVINE BLASTOCYSTS

Abnormalities of the placenta are a major factor contributing to early death in cloned bovine conceptuses. This is primarily due to incomplete chromatin remodeling and reprogramming of the donor nucleus. It is unknown whether genetic aberrations of genes crucial for placental development can be detected in pre-implantation cloned bovine embryos. This study looked at the expression profile of four genes in single bovine blastocysts derived from in vivo, in vitro produced (IVP), or cloning techniques, including handmade cloning (HMC) and serial HMC (SHMC). The genes studied included acrogranin, caudal type homeobox 2 (cdx2), estrogen-receptor-related receptor beta (essrb), and the mammalian relative of DnaJ (MRJ). These genes play a role in trophoblast regulation and placental development. Messenger RNA expression was analyzed by using PCR following cDNA amplification by means of SMART cDNA synthesis (Clontech, Palo alto, CA, USA). Primers were designed from homologous human and mouse sequence. PCR products were sequenced for verification. Five single blastocysts were analyzed from each of the following treatments: in vivo, IVP, HMC, and SHMC. Pooled (n = 10) IVP blastocyst cDNA produced by standard RT was used as a positive control. Grade 1 Day 7 blastocysts were selected for all treatments. Amplified cDNA was tested using control genes polyA, IFN-τ and GDF9. In vitro-produced embryos were matured, fertilized and cultured as published by Ruddock et al. (2004 Biol. Reprod. 70, 1131). Cloned HMC embryos were produced as described by Tecirlioglu et al. (2003 Reprod. Fertil. Dev. 15, 361). Serial HMC embryos were produced as per the HMC embryos, followed by a second round of nuclear transfer at the pronuclear stage. The pooled IVP, in vivo, and IVP blastocysts expressed all four genes of interest. In the HMC-cloned embryos, all four genes were expressed. However, in the SHMC cloned embryos, although MRJ was found to be expressed in all blastocysts, three of the five blastocysts did not express acrogranin. Similarly, two SHMC embryos did not express cdx2, and essrb was weakly expressed in three of the five embryos analyzed. Initial pregnancy rates of HMC and SHMC embryo transfers are similar. Further pregnancy results are pending. These results indicate that aberrations of genes crucial for placental development can be detected in single cloned blastocysts. It also suggests that failed implantation and/or placental defects may stem from patterned genetic defects in the pre-implantation embryo. An increase in the number of embryos analyzed would further strengthen results. These genes could act as markers to identify cloning techniques that produce more embryos with normal genetic profiles. The benefits of developing a screening tool to assess abnormalities in single pre-implantation embryos would be significant.
RELATIVE POTENCIES OF 50 ISOLATES OF BACILLUS THURINGIENSIS FOR LARVAE OF THE SPRUCE BUDWORM, CHORISTONEURA FUMIFERANA (LEPIDOPTERA: TORTRICIDAE)

Abstract Fifty Bacillus thuringiensis (B.t.) isolates representing K-1, galleriae, K-73, thuringiensis, aizawai, dendrolimus, tolworthi, kenyae, darmstadiensis, alesti, and entomocidus crystal antigen types were bioassayed against fifth-instar spruce budworm, Choristoneura fumiferana (Clem.), larvae. In addition, larvae reared on diet with and without aureomycin were tested for their susceptibility to B.t. The data indicated no significant differences in susceptibility to B.t. among insects reared on aureomycin or on aureomycin-free diet, but differences were evident in larval growth and mortality among untreated controls. None of the 50 isolates bioassayed was any more toxic to the budworm than is the strain used at present in commercial preparations of B. thuringiensis. Résumé Cinquante isolats de Bacillus thuringiensis (B.t.) représentant les types antigéniques à l'état cristallisé K-1, galleriae, K-73, thuringiensis, aizawai, dendrolimus, tolworthi, kenyae, darmstadiensis, alesti et entomocidus ont été testés contre des larves au cinquième stade de la tordeuse des bourgeons de l'épinette, Choristoneura fumiferana (Clem.). De plus, la vulnérabilité envers B.t. des larves élevées avec une alimentation additionnée ou exempte d'auréomycine a été examinée. Les résultats n'indiquent aucune différence quant à la vulnérabilité des larves alimentées avec ou sans auréomycine, mais des différences sont apparues au niveau de la croissance et de la mortalité chez les larves témoins non traitées. Aucun des 50 isolats testés n'était plus toxique pour la tordeuse que la variété présentement employée dans des préparations commerciales.
Industrial Cultivation of Oil Bearing Rose and Rose Oil Production in Bulgaria During 21ST Century, Directions and Challenges

ABSTRACT The rose growing and flower processing is a centuries-old industry in Bulgaria which was a subject of substantial structural changes during the transitional period from state-ruled to market driven economy in the 1990s. The industry successfully passed in the 21st century becoming more open and dynamic. Here we review the industrial cultivation of oil-bearing roses in Bulgaria, the recent developments, current challenges and opportunities for future development.
The role of planktonic ciliates in lake ecosystems

An analysis of plankton seasonal succession in large shallow eutrophic lake Vortsjarv (270 km2, mean depth 2.8 m, max. depth 6 m) is presented. Weekly samples for 1995 have been analysed using the PEG model approach. In winter, light was the main factor controlling phytoplankton growth. In early spring phytoplankton was mainly resource-controlled, competition for phosphorus being the main driving force. Ciliates (Paradileptus sp., Strobilidium sp. and Vorticella sp.) were the first herbivores which started to increase in April causing a twofold decline of phytoplankton biomass. The annual maximum of primary production (PP) in early May was probably caused by soluble reactive phosphorus (SRP), regenerated by herbivores, and stirred up from bottom sediments as a result of strong wind stress. This primary production peak provided substrate for further increase of bacterial biomass. The more abundant food supply supported the development of the second spring peak of herbivores (ciliates, rotifers, juve­ nile copepods) which was followed by the second modest "clear water phase" in late May. Silicon was depleted by the end of May causing a strong decrease in primary production of the diatom-dominated community, whereas the biomass of the cyanophytes increased under the improved nutrient conditions. Some weeks later, inorganic N was depleted and the period of N limitation with the appearance of IN­ fixing cyanophytes began. The ciliate collapse at the beginning of June coincided with the start of the cladoceran development and with the increase of other metazooplankton groups. This explains the fur­ ther decrease of the biomass of phytoplankton and bacteria in spite of their high production. Beginning from late June, silicon appeared again and SRP started to occur periodically, while inorganic N remain­ ed close to zero until November. During this period, phytoplankton development relied to a great extent on the N-fixation and N-regeneration potential. The collapse of the ciliate community in September removed the top-down control from bacteria and their biomass increased, while the development of cladocerans still suppressed phytoplankton biomass in spite of a quite high PP. In October phytoplankton biomass and chlorophyll a (Chla) increased, SRP was completely depleted by the middle of October reflecting a slow regeneration due to the declined activity of Zooplankton in cold water. In November nitrates appeared again, and silicon reached the same level as in spring. The biomass of N-fixing Aphanizomenon skujae decreased while Limnothrix redekei and L. planctonica were quite abundant together with diatoms.
Stepping stone gene flow in an estuarine-dwelling sparid from south-east Australia

Allozyme and mitochondrial DNA variation was surveyed in Acanthopagrus butcheri to examine the pattern of gene flow among estuaries in south‐east Australia. Allozymes distinguished two peripheral estuaries from the remaining six, although the pattern of genetic variation could owe more to selection than reproductive isolation, and overall structure was small (θ = 0·012). In contrast, mitochondrial DNA revealed a high degree of genetic structure (θ = 0·263), and a significant relationship with geographic isolation. Consequently, contemporary gene flow mostly between adjacent estuaries, consistent with a one‐dimensional stepping stone model, is evident in south‐east Australia. The data indicate that management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries.
Influence of cultivar and year on phytochemical and antioxidant activity of potato (Solanum tuberosum L.) in Ontario

Hu, C. , Tsao, R. , Liu, R. , Sullivan, J. A. and McDonald, M. R. 2012. Influence of cultivar and year on phytochemical and antioxidant activity of potato (Solanum tuberosum L.) in Ontario. Can. J. Plant Sci. 92: 485–493. Phytochemicals in coloured vegetables are responsible not only for the colour, but also for nutritional quality. In this study 11 cultivars of potato, with a wide range of skin and flesh colours, grown over two years were tested for the total phenolic content (TPC), total anthocyanin-content (TAC) and total antioxidant activity (TAA). Results showed significant variations among cultivars for both years. TPC was 1.2–3.6 mg gallic acid equivalent (GAE) g−1 dry weight (DW) in 2008 and 0.98–2.81 mg GAE g−1 DW in 2009. Total anthocyanin content was 0.70–1.92 mg cyanidin-3-glucoside equivalent (Cy3g E) in 2008 and 0.05 –1.52 mg Cy3g E g−1 DW in 2009, respectively. The TAA also varied among different potato cultivars, with values of 12 to 64 and 6.3 to 20 µmol ascorbic acid equivalents (AAE) g−1 D.
First and easternmost record of Molossops temminckii (Burmeister, 1854) (Chiroptera: Molossidae) for the state of Paraíba, northeastern Brazil

This study provides the easternmost record of Molossops temminckii (Burmeister 1854), and the first for the state of Paraiba, northeastern Brazil. These records were based on the capture of six specimens, three males and three females. The morphometric data and morphological characters were consistent with those described in the literature. This record extends the distributional range of the species approximately 470 km eastwards.
The first anatomical description of two trigonostomatine Cancellariidae, Scalptia androyensis and Scalptia foveolata (Mollusca: Gastropoda: Neogastropoda: Cancellarioidea)

Abstract Cancellariidae is a poorly known family of Neogastropods, including about 300 soft-bottom dwelling species, with a cosmopolitan distribution. As cancellariids are seldom found alive, anatomical data on this family are limited. In particular, no anatomical descriptions have been available thus far for the trigonostomatine group, a conchologically well-defined monophyletic lineage of Cancellariidae that was given a subfamilial rank in former classifications. This is the first description of the anatomy of two closely related and conchologically very similar trigonostomatine Cancellariidae: Scalptia androyensis and S. foveolata. Evident differences were detected in these two species, including the shape and arrangement of the salivary glands, the relative size of the mid and posterior oesophagous, and the structure of the pallial oviduct. Such an unexpected degree of anatomical differentiation, if more widespread in cancellariids, may prove useful in species identification of conchologically similar taxa. Instead, different shell colour morphs of S. androyensis did not display anatomical differences, corroborating the hypothesis that they are conspecific.
Stock structure delineation using variation in otolith chemistry of snakehead, Channa punctata (Bloch, 1793), from three Indian rivers

Summary Otolith chemistry was used to study the stock structure of Channa punctata collected from the River Ganga and its tributaries, the rivers Yamuna and Gomti. Whole sagittal otoliths were subjected to acid digestion to analyse the trace elements (Ca, Na, Mg, Sr, Mn, Ba, Fe and K) using ICP-AES. Data were subjected to appropriate statistical treatments, such as univariate anova, ancova, manova and DFA in order to delineate the fish stock(s) accurately. Mean concentrations of Ca, Mg, Sr, Mn, Ba, Fe and K in the otoliths of the fish from selected sites of the different rivers were significantly (P 0.05). In classification statistics, 96% of individuals were correctly classified to their original groups. The scatter plot of DF-I vs DF-II depicted the presence of different stocks in the River Ganga and its selected tributaries. Variations in the microchemistry of the otoliths showed the presence of four C. punctata stocks in the three selected rivers.
Rhizome and herbage production of endophyte-removed tall fescue clones and populations

(.) This study was conducted to determine the effect of endophyte removal on rhizome and herbage production of clones and populations of tall fescue. Six clones and four populations («Kentucky 31», Georgia-5, Georgia-Jesup, and Georgia-Jesup Improved), infected with A. coenophialum and the same clones and populations with the endophyte removed were evaluated for rhizome production, tillering, and herbage and root yield after 12 wk of growth in the greenhouse. (.)