Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of Mitochondria from Potato Tubers

1Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark; 2Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-Columbia, Columbia, USA; 3Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-Colum, Columbia, USA; 4Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; 5Institute of Biological Chemistry, Washington State University, WA, USA *For correspondence: ian.max.moller@agrsci.dk
Gracilaria apiculata and G. flabelliformis (Gracilariaceae, Rhodophyta): restoring old names for common tropical western Atlantic species, including the recognition of three new subspecies, and a replacement name for G. lacinulata

Le genre Gracilaria (Gracilariales, Rhodophyta) est depuis longtemps un des groupes d'algues rouges dont la taxinomie est un perpetuel defi ; ceci est du au grand nombre d'especes, au petit nombre de caracteres distinctifs et a une grande plasticite morphologique des caracteristiques reproductrices et vegetatives. Recemment, des phylogenies basees sur l'analyse des, sequences d'ADN du gene chloroplastique rbcL ont resolu de nombreuses questions systematiques dans le genre. La presente etude fournit une phylogenie construite a partir de l'analyse du gene rbcL de la lignee la plus derivee de Gracilaria sensu stricto, cet ensemble contenant l'espece type du genre, G. bursa-pastoris. Dans ce clade, deux especes peu connues et passees inapercues de Gracilaria : G. flabelliformis et G. apiculata, sont apparues comme deux taxons du genre, tres communs dans l'Atlantique tropical occidental. Gracilaria apiculata appartient au complexe G. cervicornis, un clade compose d'especes tres ramifiees avec des axes principaux de section circulaire a aplatie. G. flabelliformis, en revanche, appartient a un clade compose seulement d'especes atlantiques aplaties. Pour chacune de ces especes, des phenotypes extremement distincts ont ete observes dans notre circonscription des taxons ; il sont decrits comme de nouvelles sous-especes pour chacune desquelles une caracterisation detaillee est donnee : G. flabelliformis subsp. aionana subsp. nov., G. flabelliformis subsp. simplex subsp. nov., G. apiculata subsp. candelabriformis subsp. nov., et G. isabellana nom. nov., pour remplacer G. lacinulata (Vahl) Howe. un homonyme de G. lacinulata (Kutzing) Piccone.
Tumor Suppressor p53 Response To UV Light In Normal Human Keratinocyte Strains From Different Individuals

iv List of figures . x List of abbreviations . xii Chapter 1: Introduction . 1 1.1 Human Papillomaviruses (HPVs) . 1 1.2 HPV genome . 2 1.3 Mode of transmission . 3 1.4 HPV infection and life cycle . 4 1.5 Tumor suppressor protein p53 . 6 1.6 The HPV E6 protein.8 1.7 The HPV E7 protein.10 1.8 HPV associated carcinogenesis . 12 1.9 HPV vaccines . 19 1.10 Hypothesis and rationale . 21
DNA barcoding supports reclassification of Japanese Chironomus species (Diptera: Chironomidae)

Non‐biting midges (Diptera: Chironomidae) adapt to species‐specific environmental conditions and hence are promising bioindicators for aquatic and ecotoxicological monitoring. Although their utility for these purposes was historically limited by difficulties in their morphological identification, DNA barcoding offers a possible solution. Here, eight Japanese species of the genus Chironomus, which is characterized by its worldwide distribution and abundance among Chironomidae, were subjected to DNA barcoding using cytochromec oxidase subunit I (COI). To examine whether this DNA barcode is a useful indicator for Japanese species of Chironomus, we calculated genetic distances within and between the COI sequences of Chironomus species both from this study and worldwide and constructed phylogenetic trees. Based on 415 bp COI sequences and the Kimura two‐parameter model, the average genetic distances within 37 species and between 72 species were 2.6% and 17.2%, respectively. Although the ranges of genetic distances within and between species overlapped from 0.8% to 17.3%, 99.7% of average genetic distances between species were >3.0%. Some of this overlap is attributable to distances within species that were “too large” as well as those between species that were “too small”. Of eight Japanese species examined, two showed genetic distances between species that were below a 3.0% threshold, and four had distances within species that were greater than 3.0%. These results suggest a possible reclassification of these species and the need for further sampling to unveil biogeographic variations among different countries and regions.
‘NuMex BR1’ Onion

‘NuMex BR1’ is a Yellow Grano-type cultivar of short day onion (Allium cepa L.) resistant to premature seedstalk formation (bolting) and to pink root disease caused by Pyrenochaeta terrestris (Hans), Gorenz, Walker, and Larson. It was developed for fall planting where bolting is a serious problem. ‘NuMex BR1’ may be planted 10 days earlier than other Yellow Grano-type cultivars. The early planting facilitates stand establishment, and the large over-wintering plants sustain relatively low v/inter plants loss (4). On fields heavily infested with P. terrestris, the early planting results in increased yields. With large over-wintering plants and rapid plant development in the late winter and early spring, the early-planted onions attain large size before pink root becomes a serious problem. P. terrestris has a high temperature optimum (about 28°C) (2) and is relatively inactive in cold soils.
Metabolic response of Pseudomonas putida to increased NADH regeneration rates

Pseudomonas putida efficiently utilizes many different carbon sources without the formation of byproducts even under conditions of stress. This implies a high degree of flexibility to cope with conditions that require a significantly altered distribution of carbon to either biomass or energy in the form of NADH. In the literature, co‐feeding of the reduced C1 compound formate to Escherichia coli heterologously expressing the NAD+‐dependent formate dehydrogenase of the yeast Candida boidinii was demonstrated to boost various NADH‐demanding applications. Pseudomonas putida as emerging biotechnological workhorse is inherently equipped with an NAD+‐dependent formate dehydrogenase encouraging us to investigate the use of formate and its effect on P. putida’s metabolism. Hence, this study provides a detailed insight into the co‐utilization of formate and glucose by P. putida. Our results show that the addition of formate leads to a high increase in the NADH regeneration rate resulting in a very high biomass yield on glucose. Metabolic flux analysis revealed a significant flux rerouting from catabolism to anabolism. These metabolic insights argue further for P. putida as a host for redox cofactor demanding bioprocesses.
Nutrimentos y carbohidratos en plantas de Agave angustifolia Haw. y Agave karwinskii Zucc* Nutrients and carbohydrates in plants from Agave angustifolia Haw. and Agave karwinskii Zucc

Most agave species used for the production of mezcal in Oaxaca, develop on terrains with steep slopes, stony and soils of low fertility; however, is not common to fertilize agave crops, so it is necessary to know the nutritional status of the adult plants that are harvested. The objective of this research was to determine nutrient concentration in leafs and stems; morphological traits and total reducing sugar (TRS) in pinas (stem and base of leafs), from adult plant of Agave angustifolia Haw and A. karwinskii Zucc. The research was conducted in 2010 in four locations in the state of Oaxaca. In plants that farmers selected and harvested, morphological characteristics were recorded of its stems, leaf and stem samples were taken for laboratory analysis. The results showed that the pinas of Agave angustifolia Haw and A. karwinskii Zucc had an average of 80.87 and 22.59 kg fresh weight, 37.10 and 20.21 cm in diameter, 67.23 and 97.47 cm in length; the nutrient content in leaf tissues (mg g -1 dry weight) was 8.68 and 8.99 N, 1.26 and 1.61 P, 8.97 and 8.85 K, 40.26 and 66 Ca In pinas the nutrient content (mg g -1 dry weight) was 4.30 and 5.33 N, 0.28 and 0.33 P, 1.58 and 2.75 K, 10.25 and 10.13 Ca. From the fresh weight of the pinas of Agave angustifolia and A. karwinskii 21.16% and 27.29% were TRS respectively.
Some notes on yield and protein responses to nitrogen in bread and durum wheats

This paper summarises the results of 6 years trials in Canterbury with various milling wheat and pasta varieties. Yield and protein responses to timing of nitrogen application are reported. There are significant seasonal, site and cultivar effects which determine the relative yield and protein responses to the timing of applied nitrogen. The use of foliar applied liquified urea was a treatment in a number of these trials, and was effective in increasing grain protein content.
The evolution of antarctic fishes : questions for consideration and avenues for research

Cet article est tire d'une conference qui a ete donnee au cours d'un workshop intitule Technical and Theoretical Approaches to Antarctic Fish Evolution. Ce workshop s'est deroule a Santa Margherita (Ligure, Italie) du 8 au 10 octobre 1994 et etait soutenu financierement par un European Science Foundation Network Proposal intitule Fishes of the Antarctic Ocean. Cet article introduit le theme du Workshop et s'interesse plus particulierement aux aspects de l'evolution des Notothenioidei: 1) les fossiles Cenozoique des poissons en Antarctique avec une hypothese sur l'emergence des Notothenioidei ; 2) la composition de la faune moderne ; 3) une comparaison des diversifications subies par les Notothenioidei et d'autres Teleosteens ; 4) la nature des adaptations a l'environnement marin antarctique. Les objectifs suivants sont recommandes pour de futures recherches multidisciplinaires sur les Notothenioidei : 1) la construction de cladogrammes resolus au niveau du genre et de l'espece ; 2) la comparaison de cladogrammes construits a partir de differentes bases de donnees et la combinaison de differents types de caracteres en une seule grande banque de donnees ; 3) l'extension de la base taxinomique et des suites de caracteres disponibles pour l'analyse cladistique ; 4) l'evaluation des roles de la phylogenese et de l'adaptation a l'environnement dans la diversification des Notothenioidei; 5) l'utilisation de temps de divergences obtenus a partir de donnees moleculaires pour evaluer les changements du paleoenvironnement comme des evenements vicariants influencant la diversification des Notothenioidei ; 6) la poursuite de recherches centrees a la fois sur les niveaux de la micro et de la macroevolution et 7) l'incorporation des donnees sur la biodiversite marine dans la recherche sur les Notothenioidei.
COMPARATIVE BIOLOGY OF POTATO PSYLLID, BACTERICERA COCKERELLI (HEMIPTERA: TRIOZIDAE) HAPLOTYPES

By Tariq Mustafa, Ph.D. Washington State University December 2014 Chair: Richard S. Zack Zebra chip, a new and economically important disease of potato, is threatening potato production in the United States, Mexico, Central America, and New Zealand. The disease is associated with the bacterium ‘Candidatus Liberibacter solanacearum’ (Lso), vectored by potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). This insect pest feeds on over 40 plant species, including cultivated and wild solanaceous plants. Recent discoveries of four genetic variants (haplotypes) of potato psyllid, coupled with the finding that it overwinters in the Pacific Northwest on bittersweet nightshade (Solanum dulcamara), may complicate management of this psyllid, if differences exist in biological traits among the haplotypes. The present study compared development and reproduction among three psyllid haplotypes (Central, Western, and Northwestern) commonly found on Pacific Northwest potato crops, when reared on potato or bittersweet nightshade. Lso transmission efficiency among the three haplotypes was also assessed. The results showed that development time was longer for psyllids reared on nightshade than potato. The duration of the pre-oviposition period, egg incubation requirements, nymphal development time, and total developmental time was higher on bittersweet nightshade compared
Changes in protein profile under sodium chloride and boron toxicity stress in seedlings of two wheat cultivars

Two genotypes of wheat (Triticum aestivum L.), a salt tolerant KRL 1-4 and a salt sensitive HD 2329 were subjected to stress treatments of control, 10 mM B, 120 mM NaCl and 10 mM B+ 120 mM NaCl at the seedling stage in a BOD incubator at 26±1 °C for 96 h. Proteins from coleoptile and radicle were resolved by SDS-PAGE. In tolerant cultivar (KRL 1-4), two proteins of 83.6 and 28.1 kDa appeared in the coleoptile and a 35 kDa protein appeared in the radicle in the seedlings treated with B and B+NaCl. Similarly, 46.6 kDa protein was observed in the radicle of KRL 1-4 only in B treated seedlings. These results clearly indicate characteristically B induced proteins. Two proteins of 74.2 and 48.8 kDa in HD 2329 coleoptile and a 64.6 kDa protein in the radicle of both KRL 1-4 and HD 2329 seedlings were seen specific to salt treatment and were absent in boron treated seedlings. Likewise, a 70 kDa protein in the coleoptile profile of KRL 1-4 seedlings was expressed only with salt treatment, but was absent in boron treatment.
Studies on different species of plant parasitic nematodes attacking vegetable crops grown in Afikpo North L.G.A, Nigeria

nematodes recovered, including; Meloidogyne incognita with the highest prevalence of 45 (37.50%), M. hapla 32 (26.67%), Pratylenchus spp . (migratory) 25 (20.83%) and Heterodera spp. 18(15.00%). The other three species of nematodes recovered were ectoparasitic nematodes, including; Xiphinema spp. , with the highest prevalence of 20(41.67%) which is a migratory nematode; Dolichorus spp. (also migratory) 16(33.3%) and Trichodrous spp. 12(25.00%). However, okra, cucumber, garden eggs, alfalfa, tomatoes, pepper, fluted pumpkin, etc where some vegetable crops attacked by nematodes from the study area.
A new species of Chlorophytum (Asparagaceae) from the succulent Karoo biome, Namibia – with an updated key for Chlorophytum of Namibia

Until recently (Angiosperm Phylogeny Group 2009), the genus Chlorophytum Ker-Gawl. was referred to family Anthericaceae J.G. Agardh, a segregate of Liliaceae s. lat. (see Dahlgren et al. 1985). The genus, together with several others from related families, was recently placed in family Asparagaceae (subfam Agavoideae, Angiosperm Phylogeny Group 2009), and is now one of the largest genera of that family. With more than 200 species, and with a wide tropical and subtropical Old World distribution, Chlorophytum has its center of variation in tropical and subtropical Africa (Kativu & Nordal 1993, Bjorå 2008). The generic circumscription of the group was reviewed for tropical African taxa by Obermeyer (1962), Marais & Reilly (1978), Nordal et al. (1990) and Kativu & Nordal (1993). The latter transferred most of the tropical African species previously referred to the genus Anthericum L. to Chlorophytum. In tropical and subtropical southern Africa, Kativu et al. (2008) enumerated 56 species of Chlophytum for Flora Zambesiaca. Obermeyer (1962) had previously recorded 37 species (seventeen from Anthericum sensu Marais & Reilly (1978), and twenty from Chlorophytum s. str. ) from South Africa. Recently, Kativu et al. (2012) presented twelve species for Flora of Namibia. Details on the taxonomic history of Chlorophytum are provided in Marais & Reilly (1978), Kativu & Nordal (1993) and Bjorå et al. (2008). Since its generic re-circumscription (Kativu & Nordal 1993), studies on Chlorophytum provided descriptions for several new taxa from across Africa: nine new species from the Horn of Africa in Nordal & Thulin (1993), four new species from central and East Africa in Kativu (1993a), one new species from south-eastern Africa in Nordal & Poulsen (1998), two new species from Ethiopia by Sebsebe & Nordal (in Sebsebe et al. 2005), four new species from Zambia and Malawi in Bjorå et al. (2008), and one new species from Burundi and Tanzania (Meerts 2011). Information on phylogenetic relationships in genus Chlo­ rophytum is limited. Kativu (1993b) presented preliminary results of a cladistic analysis on 93 species of the genus based on morphological, anatomical and cytological characters. The study poorly supported some of the traditional generic groups (Dasystachys, Baker 1878, Anthericum sensu Marais & Reilly 1978 and Chlorophytum sensu Marais & Reilly 1978), though with extensive homoplasy. Bjorå et al. (2008) carried out a DNA-based phylogenetic analysis of Chlorophytum from representative subgroups of the genus in which they evaluated the taxonomic affinities of some four newly described species. Meerts & Bjorå (2012) used DNA
Photosynthesis and water-use efficiency of two sandhill oaks following additions of water and nutrients

VAITKUS, M. R. AND K. W. McLEOD (Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802). Photosynthesis and water-use efficiency of two sandhill oaks following additions of water and nutrients. Bull. Torrey Bot. Club 122: 30-39. 1995. -Water and nutrients are considered the primary factors limiting vegetative growth in many plant communities. We examined the effects of added water and nutrients on photosynthesis and water use efficiency (WUE) of juveniles of Quercus hemisphaerica and Quercus laevis growing together in a sandhill community in South Carolina. Supplemental water and nutrients were added in a 2 x 2 factorial design. Diurnal photosynthesis was determined approximately biweekly from June to October and integrated long-term WUE was evaluated using carbon isotope discrimination at the end of this period. Analysis of diurnal photosynthesis curves indicated no significant differences between species, but differences within species were significant between day of sampling, time of measurement, and treatment. Net photosynthesis of Q. hemisphaerica in watered treatments was significantly greater than photosynthesis in unwatered treatments, primarily at midday on days with high temperatures following prolonged drought. Neither nutrients nor water significantly affected the photosynthesis of Q. laevis, regardless of environmental conditions. Fertilization was found to differentially affect WUE of Q. hemisphaerica and Q. laevis, possibly confounding WUE differences between these two species. Because Q. hemisphaerica is often found in more mesic environments than Q. laevis, and because it responded to the addition of water with an increase in photosynthesis, we concluded that in a sandhill community Q. hemisphaerica juveniles are limited primarily by water rather than by low fertility. Our results indicated that juveniles of Q. laevis, the community dominant, are not as plastic as Q. hemisphaerica in their response to fertilizer and water additions.
Influence of spectral wavelength and N:P ratio on the cell cycle of Synechococcus strain CSIRNIO1 isolated from the central Eastern Arabian Sea

The novel phycoerythrin-containing Synechococcus strain CSIRNIO1 belonging to phylogenetic clade II was isolated from the coastal Arabian Sea. Chromophore characteristics of this isolate revealed the presence of phycoerythrin I (PEI), which allows it to utilize green light efficiently. The DNA distribution data indicate a bimodal slow growth model synchronized with the light/dark cycle. The duration of the cell cycle was regulated by spectral wavelength and nutrient concentration. Nitrate and phosphate enrichment shortened G1 phase duration when cells were exposed to equal doses of photosynthetically usable radiation (PUR) of different spectral wavelengths. G2 phase duration was influenced by spectral quality and phosphate concentration. S phase duration was not affected by the spectral wavelength. However, a shorter doubling time corresponding to shortened G1 and S phases was observed under nitrate enrichment. Phosphate enrichment resulted in shortening of all three phases (G1, S and G2). More efficient utilization of green and red light than blue light regulated the duration of the cell cycle as well as the doubling time, suggesting spectral selectivity in this strain. The effects of spectral wavelengths under varying nutrient concentrations will determine the proliferation of Synechococcus and its adaptation to different environmental conditions.
Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100-seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100-seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17-2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5-1, qSW14-1, qSW15-1 and qSW15-2, found to be the novel QTLs. A two-dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.
Comparative assessment of ecosystem C exchange in Miscanthus and reed canary grass during early establishment

Land‐use change to bioenergy crop production can contribute towards addressing the dual challenges of greenhouse gas mitigation and energy security. Realisation of the mitigation potential of bioenergy crops is, however, dependent on suitable crop selection and full assessment of the carbon (C) emissions associated with land conversion. Using eddy covariance‐based estimates, ecosystem C exchange was studied during the early‐establishment phase of two perennial crops, C3 reed canary grass (RCG) and C4 Miscanthus, planted on former grassland in Ireland. Crop development was the main determinant of net carbon exchange in the Miscanthus crop, restricting significant net C uptake during the first 2 years of establishment. The Miscanthus ecosystem switched from being a net C source in the conversion year to a strong net C sink (−411 ± 63 g C m−2) in the third year, driven by significant above‐ground growth and leaf expansion. For RCG, early establishment and rapid canopy development facilitated a net C sink in the first 2 years of growth (−319 ± 57 (post‐planting) and −397 ± 114 g C m−2, respectively). Peak seasonal C uptake occurred three months earlier in RCG (May) than Miscanthus (August), however Miscanthus sustained net C uptake longer into the autumn and was close to C‐neutral in winter. Leaf longevity is therefore a key advantage of C4 Miscanthus in temperate climates. Further increases in productivity are projected as Miscanthus reaches maturity and are likely to further enhance the C sink potential of Miscanthus relative to RCG.