Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Assessment of Taxonomic Uncertainty in Painted Turtles

Abstract There is ongoing uncertainty regarding the taxonomic status of Painted Turtles (genus Chrysemys). Most recently, a phylogenetic analysis of the mitochondrial DNA control region (mtCR) resulted in the elevation of a subspecies to the species level, resulting in two species being tentatively, but not universally, accepted: Chrysemys dorsalis and C. picta, the latter encompassing the three remaining subspecies. Here, we used expanded range-wide sampling and character data from PAX-P1 nuclear intron (n = 127) and mtCR (n = 259) to further investigate taxonomic uncertainty and paleogeography of Painted Turtles. We found five mtCR characters that distinguished C. dorsalis from C. picta; no such evidence was found in PAX-P1. Chrysemys dorsalis formed a monophyletic group in the reconstructed phylogenetic trees, whereas there was no genetic evidence for the distinctiveness of the three C. picta subspecies. The mtCR network showed C. dorsalis and C. p. bellii to each form relatively distinct clusters, whereas no clustering by morphotype was found in the PAX-P1 network. Lower levels of haplotypic diversity across the range of C. p. bellii are consistent with recent postglacial expansion to the west; however, observed mismatch distributions were multimodal, which does not indicate population expansion. Overall, the addition of nuclear DNA character data and expanded sampling support the tentative designation of C. dorsalis and C.picta (encompassing C. p. picta, C. p. bellii, and C. p. marginata) as separate species. Yet, lack of accompanying morphological data and potential for oversplitting due to targeting only individuals within the core of morphotype ranges suggests that further study is warranted.
THE ROLE OF COPROPHAGOUS BEETLES ON DUNG DECOMPOSITION AND ENHACEMENT SOIL FERTILITY: EFFECT OF BODY SIZE, SPECIES DIVERSITY AND BIOMASS

Penelitian ini bertujuan untuk menganalisis pengaruh keragaman spesies, ukuran dan biomassa kumbang koprofagus dalam merombak kotoran hewan dan meningkatkan kesuburan tanah. Percobaan dilakukan menggunakan Rancangan Acak Lengkap dengan perlakuan jumlah dan panjang tubuh spesies kumbang koprofagus. Peubah tergantung yang diamati adalah persentase kotoran yang terdekomposisi dan kadar bahan organik serta N,P,K total tanah sebagai indikator kesuburan tanah. Hasil penelitian menunjukkan bahwa persentase kotoran hewan yang terdekomposisi lebih dipengaruhi oleh ukuran dan biomassa kumbang yang terlibat dibandingkan dengan jumlah spesies. Persentase kotoran yang terdekomposisi berkorelasi positif dengan ukuran kumbang koprofagus. Kadar N,P,K total tanah meningkat mengikuti jumlah kotoran hewan yang terdekomposisi yang mengindikasikan bahwa aktifitas perombakan kotoran hewan oleh kumbang koprofagus berpengaruh positif terhadap kesuburan tanah.
The levels of hormone and carbohydrate in autumn and non-autumn flowering tree peonies

Mornya, P. M. P. and Cheng, F. 2011. The levels of hormone and carbohydrate in autumn and non-autumn flowering tree peonies. Can. J. Plant Sci. 91: 991–998. This study analyzed the levels of gibberellic acid (GA3), indole-3-acetic acid (IAA), cytokinin (CTK) and abscisic acid (ABA) hormones using high-performance liquid chromatography, along with the levels of sucrose, reducing sugar and starch carbohydrates by spectrophotometer during induction, initiation and differentiation stages of bud development in autumn (AFP) and non-autumn (NAFP) flowering tree peony cultivars exhibiting variations in flowering pattern. The experimental design was a randomized complete block with three replications. The variation in flowering pattern between AFP and NAFP was largely influenced by differences in GA3, IAA and CTK levels at different bud developmental stages. The flower formation cycle was completed earlier in AFP than in NAFP, hence flowering was twice annually. Cytokinin, particularly N6-(Δ2-isopentenyl)-adenosin.
NOSTOC (CYANOPHYCEAE) GOES NUDE: EXTRACELLULAR POLYSACCHARIDES SERVE AS A SINK FOR REDUCING POWER UNDER UNBALANCED C/N METABOLISM 1

Many species of the filamentous N2‐fixing heterocyst‐forming Cyanobacteria of the genus Nostoc produce large amounts of extracellular polymeric substances (EPS), but hitherto no general model has been proposed of the factors that control their synthesis. Previously, we demonstrated a strong correlation between the presence of a glycocalyx (or EPS capsule) and diazotrophic growth in the genus Nostoc. When grown with nitrate, nude morphotypes lacking a glycocalyx were obtained for all the capsulated strains tested. CO2 availability was pro‐posed as a key factor that controls the synthesis of the capsule. To test this hypothesis, Nostoc PCC 7936 was cultured diazotrophically (N2) or with nitrate with different CO2 supplies. By tuning the pH and the supply of CO2, capsulated or nude mor‐photypes were obtained irrespective of the source of nitrogen. Exocellular polysaccharides were synthesized only when the fixed carbon exceeded the amount of nitrogen available. The glycocalyx is not needed for the optimal functioning of nitrogenase because diazotrophic cultures grew equally well, irrespective of whether they were capsulated or nude. Capsulated cultures possessed protein to carbohydrate ratios that ranged between 1 and 1.5, whereas in nude cultures the ratio ranged between 2 and 2.5. Low protein to carbohydrate ratios were indicative for either nitrogen‐limited or carbon‐oversaturated cultures. The results demonstrate that in Nostoc EPS serve as a sink for the excess fixed carbon under unbalanced C/N metabolism.
Leaf colour polymorphisms: a balance between plant defence and photosynthesis

Whether plants use leaf colour to deter herbivores remains controversial. The warning signal hypothesis predicts that red pigmentation is adaptive by reducing herbivory; plants with predominantly red foliage should have higher fitness than those with green leaves. Despite many discussions, this prediction has rarely been tested, and alternative, non‐exclusive hypotheses cannot be ruled out. We have exploited leaf colour polymorphism in Pseudowintera colorata to test the warning signal hypothesis and to address possible alternative explanations. Consistent with warning signals, redder foliage contained higher concentrations of polygodial, a sesquiterpene dialdehyde with strong antifeedant properties, and incurred less herbivory than green leaves. Redder plants hosted 22% fewer lepidopteran leafroller larvae than neighbouring green plants. However, contrary to the predictions of the hypothesis, there were no differences in fitness parameters between red and green plants. Overall leaf canopy colour was not a significant predictor of the number of seeds per fruit or of mean seed weight. This may be explained by differences in photosynthesis: green P. colorata leaves had 47% higher maximum CO2 assimilation rates than matched red leaves from neighbouring plants. These results indicate that the benefits of deterring insect herbivores by signalling may be balanced by the higher photosynthetic rate of non‐signalling plants. A balance between signalling and photosynthesis is a novel mechanism for the maintenance of leaf colour polymorphisms in nature. Synthesis. Anthocyanin pigments may simultaneously serve multiple functions within leaves, and individuals of the same plant species may use different strategies to cope with insect herbivores. Therefore, investigations into the role of these pigments in plant–insect interactions need to consider plant physiology and the diversity of plant defence mechanisms.
Mitochondrial gene diversity in Cepaea : population structure, history and positive selection

Previous studies on the geographical distributions of both shell polymorphisms and mitochondrial haplotypes in Cepaea land snails have suggested varying contributions of natural selection, random genetic drift and population history to the origin and persistence of variation. We combine previous studies of polymorphism within two species of Cepaea, with new molecular data from two mitochondrial genes. The distributions of mitochondrial variants suggest that elements of population history may have been influential in creating patterns of diversity. However, some patterns of amino acid substitution that are found in a protein coding gene are also consistent with the action of diversifying selection. This suggests the possibility that in addition to stochastic processes such as repeated founder events, local extinctions and random genetic drift within a structured population, adaptive molecular change may have affected mitochondrial diversity. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87, 167–184.
Detailed analysis of Cucurbita pepo seed coat types and structures with scanning electron microscopy

Discovery of a mutant thin-coated seed phenotype at the end of the 19th century facilitated pumpkin (Cucurbita pepo L.) seed oil production and increased botanic interest in seed coat types and their structures. The main seed coat characteristics were usually analyzed by light and fluorescent microscopy, and more recently, seed coat traits have also been mapped on a C. pepo gene map. The aim of our research was to collect and describe various pumpkin seed types and to analyze, using scanning electron microscopy (SEM), the detailed structure of their seed coats. Seeds of 29 cultivars and landraces were collected and visually evaluated based on seed coat characteristics. Seed samples belonging to different seed types discovered in our collection were transversely sectioned and analyzed by SEM. Twelve seed types were determined, and SEM analysis revealed high variability in their seed coat structures. Using SEM, tissue and cell structures were clearly visible, and novel details of cell and tissue topography .
Targeting the Effector Site with IFN-αβ-Inducing TLR Ligands Reactivates Tumor-Resident CD8 T Cell Responses to Eradicate Established Solid Tumors1

Effective antitumor CD8 T cell responses may be activated by directly targeting the innate immune system within tumors. We investigated this response by injecting a range of TLR agonists into established tumors using a mouse model of malignant mesothelioma stably transduced with the hemagglutinin (HA) gene as a marker Ag (AB1-HA). Persistent delivery of the dsRNA mimetic poly(I:C) into established AB1-HA tumors resulted in complete tumor resolution in 40% of mice, with the remaining mice also showing a significant delay in tumor progression. Experiments in athymic nude mice along with CD8 depletion and IFN-αβ blocking studies revealed that tumor resolution required both CD8 T cells and type I IFN induction, and was associated with local changes in MHC class I expression. Surprisingly, however, tumor resolution was not associated with systemic dissemination or tumor infiltration of effector CD8 T cells. Instead, the antitumor response was critically dependent on the reactivation of tumor-resident CD8 T cell responses. These studies suggest that, once reactivated, pre-existing local CD8 T cell responses are sufficient to resolve established tumors and that in situ type I IFN is a determining factor.
Constructing practical TIN with high speed based on Quad-Edge

In this paper,a kind of structure named Quad-Edge with completely spacial topological property is introduced,based on it we can construct Delaunay Triangulation and Voronoi Diagram with high speed,the construction of Constrained Delaunay Triangulation is also introduced to generate practical TIN.Based on all above,building contour line,terrain section and TIN with some hole structures are resolved to some extent.
Análisis de trazos de las especies mexicanas de rhus subgénero lobadium (angiospermae: anacardiaceae)

El subgenero Lobadium del genero Rhus posee alrededor de 25 especies, que se distribuyen principalmente en Mexico. Se analizo la distribucion geografica de estas especies aplicando un enfoque panbiogeografico, a partir de un analisis de parsimonia de endemismos. La distribucion del subgenero Lobadium se encuentra principalmente en la Zona de Transicion Mexicana, constituyendo un elemento neartico. Se obtuvieron tres trazos generalizados: 1) California-Baja California; 2) Costa del Pacifico Mexicano-Sierra Madre Occidental; y 3) Tamaulipas-Sierra Madre del Sur-Eje Volcanico Transmexicano- Altiplano Mexicano-Sierra Madre Oriental. El primero coincide con el dominio Californiano de la region Neartica, mientras que los otros dos apoyan la hipotesis de la Zona de Transicion Mexicana, en las zonas montanosas de Mexico, sitio donde se establece el contacto entre elementos bioticos nearticos y neotropicales.
Population decline in Adenostoma sparsifolium (Rosaceae): an ecogenetic hypothesis for background extinction‡

We describe a 15-year study of the loss of reproductive fitness and population decline in Adenostoma sparsifolium, a rosaceous shrub endemic in the fire-prone chaparral vegetation of southern California (USA) and adjacent northern Baja California, Mexico. Our studies of background extinction concentrated on small relict populations occurring in the eastern Santa Monica Mountains where reproduction is genetically compromised by uniquely high rates of embryonic/endosperm abortion (97–99%) resulting largely from self-pollination in highly heterozygous populations. Environmental factors further reduce reproductive fitness. The relatively few viable seeds produced are not well adapted to survive wildfires that are a regular (approximately 21 years) occurrence in chaparral. Seedling recruitment after burning is rare and any established seedlings ultimately die from the annual 4–9-month summer droughts typical of Mediterranean climates. Adult mortality is manifest from wildfire (approximately 6%) and occasional multiple-year droughts (approximately 15%). Given the virtual absence of new post-fire reproduction and a low but persistent rate of adult mortality, slow population demise resulting in background extinction is inevitable. We posit that A. sparsifolium is ecologically ‘out of place’ in the present chaparral environment and appears best adapted to a moister climate with summer rains and few wildfires that prevailed before the increasing aridity and warming from mid-Holocene to the present. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 269–292.
Structure and Function of Carbamoylphosphate Synthase

The Km-values for ammonium and bicarbonate in carbamoylphosphate synthesis are 1.1 mM and 5.3 mM respectively at saturation with ATP and acetylglutamate. The are independent of the concentration of the second substrate. The same Km for bicarbonate is found in the hydrolysis of ATP, which is catalyzed by the enzyme in the absence of ammonium. The [32P]orthophosphate–ATP-exchange, which is very slow, requires bicarbonate and ammonium. With these findings, the following mechanisms for the C–N-ligase step(s) of the enzyme are possible: (a) enzyme-bound carbamate is formed by a simultaneous reaction of ATP, bicarbonate and ammonium; (b) at first enzyme-bound “active CO2” is formed in a rapid and reversible reaction, which releases both the ATP-products, ADP and orthophosphate only upon the reaction with ammonium. Possible structures for this intermediate would be carboxyphosphate plus ADP and the addition compound of bicarbonate with ATP (with penta-coordinated phosphorus). The participation of biotin was excluded. As can be estimated from the kinetic findings, only a small fraction of the enzyme molecules would ever be charged with “activity, CO2”; the half-time of its decomposition, as calculated from the ATPase activity, would be ≤ 2 sec.
Biology, Epidemiology and Management of the Pathogenic Fungus Macrophomina phaseolina (Tassi) Goid with Special Reference to Charcoal Rot of Soybean (Glycine max (L.) Merrill)

The fungus Macrophomina phaseolina is a causative agent of diseases in more than 500 plant species. The fungus is primarily soil-inhabiting but is also seed-borne in many crops including soybean. It survives in the soil mainly as microsclerotia that germinate repeatedly during the crop-growing season. Low C : N ratio in the soil and high bulk density as well as high soil moisture content adversely affect the survival of sclerotia. The disease can be managed to some extent by cultural practices, organic amendments, seed treatment and genetic host resistance. The scattered literature on these aspects is reviewed in this paper.
Suppression of methanogenesis by dissimilatory Fe(III)‐reducing bacteria in tropical rain forest soils: implications for ecosystem methane flux

Tropical forests are an important source of atmospheric methane (CH4), and recent work suggests that CH4 fluxes from humid tropical environments are driven by variations in CH4 production, rather than by bacterial CH4 oxidation. Competition for acetate between methanogenic archaea and Fe(III)‐reducing bacteria is one of the principal controls on CH4 flux in many Fe‐rich anoxic environments. Upland humid tropical forests are also abundant in Fe and are characterized by high organic matter inputs, steep soil oxygen (O2) gradients, and fluctuating redox conditions, yielding concomitant methanogenesis and bacterial Fe(III) reduction. However, whether Fe(III)‐reducing bacteria coexist with methanogens or competitively suppress methanogenic acetate use in wet tropical soils is uncertain. To address this question, we conducted a process‐based laboratory experiment to determine if competition for acetate between methanogens and Fe(III)‐reducing bacteria influenced CH4 production and C isotope composition in humid tropical forest soils. We collected soils from a poor to moderately drained upland rain forest and incubated them with combinations of 13C‐bicarbonate, 13C‐methyl labeled acetate (13CH3COO−), poorly crystalline Fe(III), or fluoroacetate. CH4 production showed a greater proportional increase than Fe2+ production after competition for acetate was alleviated, suggesting that Fe(III)‐reducing bacteria were suppressing methanogenesis. Methanogenesis increased by approximately 67 times while Fe2+ production only doubled after the addition of 13CH3COO−. Large increases in both CH4 and Fe2+ production also indicate that the two process were acetate limited, suggesting that acetate may be a key substrate for anoxic carbon (C) metabolism in humid tropical forest soils. C isotope analysis suggests that competition for acetate was not the only factor driving CH4 production, as 13C partitioning did not vary significantly between 13CH3COO− and 13CH3COO−+Fe(III) treatments. This suggests that dissimilatory Fe(III)‐reduction suppressed both hydrogenotrophic and aceticlastic methanogenesis. These findings have implications for understanding the CH4 biogeochemistry of highly weathered wet tropical soils, where CH4 efflux is driven largely by CH4 production.
Sodium Chloride-Induced leaf senescence in Hydrocotyle bonariensis Lam. and Foeniculum vulgare L.

Leaf senescence induced by sodium chloride was studied in Hydrocotyle bonariensis Lam. and Foeniculum vulgare L. Both species belong to Umbelliferae family, however only H. bonariensis grows spontaneously in sandy soils of coastal regions (saline soils). Leaves of plants receiving nutrient solutions containing different concentrations of NaCl were evaluated for fresh and dry weights and chlorophyll content. The denaturating electrophoretic profiles of leaf proteins were also studied. Sodium chloride changed the protein profile of F. vulgare and hastened the leaf senescence of both the species. However, plants of H. bonariensis receiving 599 mM NaCl lasted longer than F. vulgare. Therefore, the occurrence of H. bonariensis in saline soils might be related with mechanisms of salinity tolerance.
Movement behaviour of adult western toads in a fragmented, forest landscape

Habitat loss and fragmentation are among the best documented explanations for the dramatic declines amphibians are experiencing globally. The western toad (Anaxyrus boreas (Baird and Girard, 1852)) is an IUCN red-listed species whose distribution range has been significantly affected by habitat modification. We used radiotelemetry to follow daily, postbreeding movement patterns of 23 adult male toads in a fragmented landscape near Vancouver, British Columbia, Canada, composed of forest patches and small, recent clearcuts (~5 ha). Results showed that toads in forests oriented towards edges of clearcuts from at least as far as 150 m. Greater than 60% of toads released in forest patches chose to enter the clearcuts from adjacent forests, indicating high boundary permeability. Net displacement distance was not significantly reduced in these clearcuts; however, movement rates were significantly lower on clearcuts than in forest. This indicates that there is no structural impediment to movements; however, there.
Powdery Encapsulation of d-Limonene by Kneading with Mixed Powders of β-Cyclodextrin and Maltodextrin at Low Water Content

To enhance the storage stability of essential oils such as d-limonene, a mixed powder of β-cyclodextrin and maltodextrin was used to encapsulate the liquid flavor in a powder state. In this study, powdery encapsulation of d-limonene was done by direct kneading of d-limonene with the mixed powder at low water content, using a twin screw kneader. The retention of d-limonene in the periodically sampled powder reached a maximum when the mass ratio of β-cyclodextrin to maltodextrin in the mixed powder equaled unity and the initial molar ratio of d-limonene to β-cyclodextrin was larger than unity. From X-ray diffraction of the powder, it could be guessed that the maximum retention of d-limonene might come from the adsorption of d-limonene upon maltodextrin. The equilibrium retention of d-limonene in the dry powder depended not only upon the mass ratio of β-cyclodextrin to maltodextrin in the mixed powder, but upon the initial moisture content in the powder. The equilibrium retention could be estimated well by a.
Recent Updates on Salinity Stress in Rice: From Physiological to Molecular Responses

One-fifth of irrigated agriculture is negatively affected by high soil salinity. The expected population growth, over 9 billion by 2050, enhances the pressure for agricultural production in marginal saline lands. Rice (Oryza sativa L.), the staple food for more than half of the world's population, is the most salt-sensitive cereal. The need for salt-tolerant rice varieties able to cope with several other stress conditions obviously puts a lot of pressure on breeders who must better comprehend the physiology and genetic control of salt tolerance. In spite of several good reviews recently published, an integrated vision of current information on rice tolerance to salt stress has been lacking. Here we present the most recent data on the salinity effect on rice physiology and stress adaptation, including implications on growth regulation and reproductive development. We have included an inventory of salt tolerance donors available for breeding programs and a comprehensive survey of current work on QTL detection and cloning as well as marker-assisted selection to introgress favorable alleles into elite rice lines. A schematic view of the rice chromosomes on which salt tolerance QTLs and candidate genes are positioned is also included. Finally, we focus on the most promising candidate genes involved in salt stress response. There, we discuss the available knowledge on salt stress signaling and ion homeostasis, LEAs and other stress-induced proteins, genes with unknown function and transcription regulators as well as the present knowledge on the role of post-translational modifications on the modulation of the response to salinity in rice. We conclude by highlighting still missing clues that could help to design better salt tolerant varieties, and we evaluate the significance of the data presented for the future of rice breeding and sustainability of the culture in marginal saline soils.