Miracle-dz/UniFAR-FTUs huggingface dataset:
Root-knot nematode staining with artificial food dyes.

The dyes used for staining nematode egg masses and eggs can cause environmental hazards and human health concerns. The aim of this study was to evaluate different artificial food dyes, as a replacement for acid fuchsin and phloxine B, for staining eggs and egg masses of Meloidogyne javanica from infected tomato plants. Five different combinations of dyes were tested at five concentrations. For control treatments, infected roots were stained with acid fuchsin and phloxine B for coloring eggs and egg masses, respectively. Egg staining with the dyes ponceau 4R with red 40 and ponceau 4R with brilliant blue, at the concentration of 4%, showed results similar to those obtained with acid fuchsin. However, egg masses were effectively stained with ponceau 4R food dyes with red 40 and with ponceau 4R with brilliant blue at all tested concentrations. Ponceau food coloring dyes gave a good contrast for nematode egg masses and egg counting, do not present human health and environmental pollution problems, and can be reused, with less waste being generated in the laboratory. These dyes are low-cost products that are available at most supermarkets, and can efficiently substitute acid fuchsin and phloxine B for staining eggs and egg masses of M. javanica.
Characterization of Nrl1 protein in Schizosaccharomyces pombe

Die Spalthefe Schizosaccharomyces pombe, ist ein idealer Modellorganismus um eukaryotischen Zelle Biologie zu studieren, da es leicht zu manipulieren, wahrend viele Gemeinsamkeiten mit hoheren Organismen wie Zentromeren mit repetitiven Sequenzen, grose Replikationsursprunge, konserviert Telomerproteine, konserviert Heterochromatin Proteine und epigenetische Silencing-Mechanismen. In dieser Studie die evolutionar konserviert Nrl1 Protein in S. pombe charakterisiert wurde und seine Rolle in pre-mRNA-Splicing und Genomstabilitat identifiziert war. Es ist gezeigt, dass, im Gegensatz zu seinen Ortholog NRDE-2 in C. elegans, Nrl1 nicht fur RNAi-Silencing und Regulierung der PolII Dehnung erforderlich ist. Stattdessen bildet Nrl1 einen Komplex mit Splice- und mRNA Verarbeitungsfaktoren und deren Loschung fuhrt zu erheblichen Veranderungen in der Splicing-Muster an mehreren genomischen Loci. Daruber hinaus es ist gezeigt, dass nrl1Δ Mutanten zeigen Merkmale von endogenen DNA-Schaden, wie langliche Zellmorphologie und Chromatin Schwitz-, zusammen mit Defekten in der Chromosomensegregation wahrend der Meiose. Da Nrl1 physisch nicht mit jedem Protein in der Chromosomensegregation und Meiose beteiligt assoziieren, ist dieser Phanotyp wahrscheinlich die Folge der indirekten Auswirkungen der Nrl1 auf die Genexpression und oder Splicing. Im Einklang mit dieser Hypothese es war gefunden, dass Nrl1 Loschung fuhrt zu Deregulierung der Schlussel Meiose Gene wie der Meiose Master-Regulator Mei2 und der Meiose-spezifische kinetochore Faktor MOA1, unter anderem. Insgesamt diesem Ergebnisse liefern neue funktionale Einblick in die Rolle des Proteins Nrl1 in pra-mRNA-Splicing und Genomstabilitat. Da Nrl1 in hoheren Eukaryoten, einschlieslich Menschen konserviert ist, erreicht dieser Studie weiter das Hefesystem. Der menschliche Ortholog von Nrl1, hNRDE-2, unten reguliert und mit Copy Number Aberrationen in Tumorzellen assoziiert darauf hindeutet, dass es als Tumorsuppressor wirken kann. Unsere Ergebnisse liefern somit die Grundlage fur zukunftige Untersuchungen auf eine mogliche Rolle von hNRDE in der Krebstherapie.
Quaternary and Recent land snails (Mollusca: Gastropoda) from Red Hills Road Cave, Jamaica

The fossil record of terrestrial animals in the Antilles is dominated by vertebrates and gastropods from Quaternary cave fills. Red Hills Road Cave (RHRC), parish of St. Andrew, Jamaica, contains a fauna circa 30,000 years old, which is unusual both for the richness of its included tetrapods and gastropods, and the exceptional, threedimensional preservation of millepedes and isopods. RHRC has yielded 62 species of Pleistocene gastropods; 50 extant species have been identified from near the cave and 12 more from elsewhere in the Red Hills, but only 30 are common to both fossil and Recent faunas. There is, thus, a marked divergence between the known Pleistocene and Recent snail faunas of this area, which results both from local extinction of Pleistocene species and immigration into the area by a significant proportion of the Recent fauna. This contrasts with previously reported molluscan cave faunas from Jamaica which have suggested that local endemic species have had much more static distributions over the same period. We interpret the changes at RHRC as indicating a reduction in precipitation from the Pleistocene to Recent. Gastropod species not previously reported from Jamaica include Ptychopatula spp. A and b, Punctum (Toltecia) vitreum Baker, Punctum (Punctum) sp. a, Radiodiscus sp. a and Radiodiscus? sp. b.
The leaf extract of Ribes nigrum L. is a potent stimulator of the endothelial formation of NO in cultured endothelial cells and porcine coronary artery rings

BACKGROUND: Endothelial dysfunction is a major hallmark of most types of cardiovascular diseases. Numerous plant extracts have been shown to cause endothelium-dependent relaxations by increasing the endothelial formation of the potent vasoprotective factor, nitric oxide (NO). OBJECTIVE: The ability of different Ribes nigrum L. extracts (Grossulariaceae) to induce endothelium-dependent relaxation by stimulating the endothelial formation of NO was assesssed. METHODS: Ribes nigrum extracts were prepared from buds, berries and leaves by extraction (Acetone:H2O:Acetic Acid; 70/28/2 (v/v/v)) and lyophilized after acetone evaporation. The ability of the extracts to stimulate the endothelial formation of NO was assessed using cultured endothelial cells and isolated porcine coronary artery rings. RESULTS: The Ribes nigrum leaf extract increased to a greater extent than the bud and the berry extracts the formation of NO, and up-regulated eNOS mRNA expression in cultured endothelial cells (the stimulatory effects amounted to 197 ± 9%, 134 ± 6% and 118 ± 5%, respectively). The leaf extract induced greater relaxations of isolated coronary arteries with endothelium than the bud and the berry extracts whereas no such effects were observed in rings without endothelium. Relaxations to the leaf extract were minimally affected by indomethacin and by inhibitors of endothelium-dependent hyperpolarization response, and markedly reduced by NG-nitro-L-arginine. CONCLUSIONS: The present findings indicate that the Ribes nigrum leaf extract is a more potent inducer of the endothelial formation of NO than the bud and the berry extracts.
Understanding ancient life: how Martin Brasier changed the way we think about the fossil record

Abstract Crucial to our understanding of life on Earth is the ability to judge the validity of claims of very ancient ‘fossils’. Martin Brasier's most important contribution to this debate was to establish a framework within which to discuss claims of the ‘oldest’ life. In particular, he made it clear that the burden of proof must fall on those making the claim of ancient life, not those refuting it. This led to his formulation of the concept of the continuum of morphologies produced by life and non-life and the considerable challenges of differentiating biogenesis from abiogenesis. Martin Brasier developed a set of criteria for distinguishing life from non-life and extended the use of many new high-resolution analytical techniques to palaeontological research. He was also renowned for his work on the Cambrian explosion and the origin of animals. Although he had spent much of his early career working on the geological context of these events, it was not until he returned to studying the Ediacaran and Cambrian periods in his later years that he began to apply this null hypothesis way of thinking to these other major transitions in the history of life. This led to him becoming involved in the development of a series of nested null hypotheses, his ‘cone of contention’, to analyse enigmatic fossils more generally. In short, Martin Brasier taught us how to formulate biological hypotheses in deep time, established the rules for how those hypotheses should be tested and championed a host of novel analytical techniques to gather the data required. As a consequence, future discussions of enigmatic specimens and very old fossils will be greatly enriched by his contributions.
Survivorship analysis of Paleozoic Crinoidea: effect of filter morphology on evolutionary rates

The evolutionary rates of Paleozoic Crinoidea were obtained using dynamic survivorship analysis. The stratigraphic ranges of 838 genera were used in the analyses, revealing a mean generic duration of 12.0 m.y. and a mean species duration of 6.7 m.y. , values within the range of longevities reported for other taxa. Further analyses showed differences in evolutionary rates among crinoid taxa: camerate species and genera were shorter-lived than species and genera of flexibles and inadunates. This pattern may result from ecological differences among these taxa: an energy budget equation solved for crinoids with various filter morphologies revealed that crinoids with fine-mesh filters require higher current velocities to supply them with sufficient particulate nutrients than do crinoids with coarse-mesh filters. A hypothesis stipulating that these differences control the distribution of crinoids among different environments is supported by patterns of occurrence of Mississippian crinoids: the pinnulate camerates (fine filter) dominate higher energy settings while the non-pinnulate inadunates and flexibles (coarse filter) are found in all environments. The “specialized” pinnulate crinoids may therefore be more prone to speciation and extinction than the non-pinnulate “generalists,” thus accounting for the observed differences in the evolutionary rates of the three subclasses. The above hypothesis was tested by comparing evolutionary rates of two morphological groups: fine-filtered crinoids (camerates) and coarse-filtered crinoids (non-pinnulate Paleozoic crinoids). As predicted, fine-filtered taxa had higher extinction and origination rates. A “bootstrapping” technique revealed that the differences in extinction rates were significant at the p < 0.10 level.
Masting synchrony in northern hardwood forests: super‐producers govern population fruit production

Trees commonly reproduce via masting cycles, which involves synchronized inter‐annual variability in fruit crop size. A few individuals in a population will commonly produce much more fruit than others. If these trees produce fruit more frequently, as indicated by a lower inter‐annual variability in fruit production, they may dominate fruit production over time. By measuring fruit production of 1635 individuals of 10 temperate tree species across 4 years in northern lower Michigan, we estimated the inter‐annual variability and synchrony in each species. We compared fruit production estimates with measurements of tree size, soil nutrient availability and neighbourhood crowding to investigate the source of inter‐individual variation in number of fruit produced. We found that trees’ fruit production increased with tree size. The trees that accounted for the largest proportion of total fruit production had lower inter‐annual variability and higher synchrony in fruit production. These ‘super‐producer’ trees tended to have high nutrient availability and few neighbouring trees, but there were no effects of nutrient availability or neighbourhood crowding on fruit production in the population as a whole. Synthesis. Masting is a population‐level phenomenon, and is typically studied at this level. However, when we apply individual tree observations of fruit production to this phenomenon, it reveals super‐producers which produce fruit more consistently than the rest of the population. By reducing inter‐annual variability in fruit production, but increasing synchrony and making large numbers of fruit, super‐producers may be able to reap the benefits of masting while governing population fruit production over time.
Seasonal Diversity of Butterflies and Its Relationship with Woody-Plant Resources Availability in an Ecuadorian Tropical Dry Forest

Understanding the seasonal community structures of highly diverse animal taxa and how they interact with plants is necessary for efficient conservation efforts such as rapid biodiversity inventory protocols and monitoring programs. This knowledge is particularly important for seasonal tropical dry forests, which are among the most threatened ecosystems on the planet. We sampled a seasonal tropical dry forest over the course of a year to determine the period of greatest butterfly richness. Additionally, we evaluated availability of potential woody plant trophic resources (flower buds, blossoms, unripe fruits, ripe fruits, and foliage) in relation to butterfly richness and community composition. Twenty of the 22 species collected showed flight activity between January-April (rainy season), coinciding with maximum plant resources availability. Lepidoptera species richness correlated positively with amount of ripe fruits and foliage. Community composition changes among sample dates involved losses and gains, and not turnovers, of species. These shifts correlate with seasonal oscillations in the variety of ripe fruits and the amount of foliage. Our results indicate that rapid inventory protocols may be applied in the period of February-March; species richness monitoring can be restricted to the rainy season (saving labor and economic costs); and ripe fruits and foliage may be suitable candidates for temporal plant-butterfly interaction surveillance.
Richness and Abundance of Aechmea and Hohenbergia (Bromeliaceae) in Forest Fragments and Shade Cocoa Plantations in Two Contrasting Landscapes in Southern Bahia, Brazil

The intensification of agricultural activity can have profound impacts on biodiversity. We evaluated the influence of the landscape's percentage of forest cover and shaded cocoa plantations on the community of zoochorous bromeliads in southern Bahia, Brazil. We selected two contrasting landscapes, one dominated by Atlantic tropical rainforest and the other by traditional cocoa plantations. In each landscape we sampled three forest fragments and three areas of cocoa plantation, where we conducted a survey of epiphytic bromeliads of the genera Aechmea and Hohenbergia in eight plots of 400 m2 in each area. The number of trees differed between landscapes and habitats, and was higher in forest fragments than in shade cocoa plantations, but the number of phorophytes was similar between landscapes and habitats. Highest richness of Aechmea and Hohenbergia species was found in forest fragments in landscapes where forests are predominant. Contrary to expectations, the richness in the other areas was relatively low, and extremely low in the landscape dominated by cocoa plantations, ranging from zero to four species per fragment. Bromeliad abundance was not different among landscapes and habitats, but the shade cocoa plantations located in predominant agroforest landscape showed the higher number of stands. Moreover, the species found in the cocoa plantations were more drought-tolerant species. These results suggest that the conservation of species of these genera depends on factors such as the conservation status of each forest fragment and the microclimatic alterations in the habitats, and not only on the percentage of forest in the landscape per se.
RKVL-318, a Root-knot Nematode-resistant Watermelon Line as Rootstock for Grafted Watermelon

The Agriculture Research Service, U.S. Department of Agriculture, announces the release of ‘RKVL-318’, a novel germplasm line useful as a rootstock and as a genetic resource for enhancing resistance to root-knot nematodes (RKNs) in watermelon cultivars. ‘RKVL-318’ is derived from the wild-type watermelon Citrullus lanatus (Thunb.) Matsum. et Nakai subsp. lanatus var. citroides (Bailey) Mansf. ex Greb. (CLC) that is indigenous to southern Africa. The ‘RKVL-318’ plants are resistant to the southern RKN (Meloidogyne incognita), peanut RKN (Meloidogyne arenaria), and Javanese RKN (Meloidogyne javanica). The watermelon plants grafted on ‘RKVL-318’ rootstock had considerable yield advantage over non-grafted watermelon plants in fields infested with RKN. ‘RKVL-318’ should be useful in breeding programs aiming to develop RKN-resistant rootstocks for grafted watermelon or to enhance RKN resistance in watermelon cultivars. ‘RKVL-318’ was developed at the USDA, ARS, U.S. Vegetable Laboratory, Charleston, SC, by Dr. Judy A. Thies, Research Plant Pathologist, and Dr. Amnon Levi, Research Plant Geneticist.
Is the circulating UK Bordetella pertussis population evolving to evade vaccine-induced immunity?

Bordetella pertussis is the causative agent of whooping cough (or pertussis) that has become resurgent worldwide. Resurgence has been linked to the introduction of acellular pertussis vaccines (ACVs) and the evolution of B. pertussis away from vaccine-induced immunity. In 2012, the United Kingdom suffered a major pertussis outbreak. I conducted whole genome sequencing and genomic analysis of 95 strains including those isolated from the UK outbreak and demonstrated that although large-scale genetic changes in B. pertussis were not the cause of this outbreak, vaccine-antigen encoding genes are evolving at higher rates than other surface protein-encoding genes, this difference becoming more pronounced since the introduction of the ACV in the UK. The dramatic increase in the frequency of pertactin (Prn)-deficient strains worldwide is possibly in response to vaccine-mediated selection pressure. However, just one Prn deficient strain was identified among the UK outbreak strains. Prn expression and IgG binding to B. pertussis obtained with post-vaccine sera was determined by flow cytometry and compared between pre-outbreak and outbreak strains, but no significant differences were observed. However, a positive correlation between Prn expression and post vaccination induced IgG binding to strains was identified, supporting the idea that strong immunological selection pressure is exerted on Prn and this is playing a role in the evolution of B. pertussis. The rapid evolution of vaccine-antigen encoding genes raises serious concerns regarding the ability of current vaccines to control pertussis.
Identification of Resistance to Peppery Leaf Spot among Brassica juncea and Brassica rapa Plant Introductions

Brassica leafy greens (Brassica juncea L. and Brassica rapa L.) represent one of the most economically important vegetable crop groups in the southeastern United States. In the last 10 years, numerous occurrences of a leaf-spot disease on these leafy vegetables have been reported in several states. This disease, known as peppery leaf spot, is now causing serious crop losses and has been attributed to the bacterial phytopathogen Pseudomonas syringae pv. maculicola (Psm). To date, it appears that all cultivars of the Brassica leafy greens are susceptible, and available pesticides for control of this disease appear unable to reduce the disease to acceptable levels. Thus, we undertook a search for potential resistance to this disease among accessions of B. juncea and B. rapa included in the U.S. Plant Introduction (PI) collection. In greenhouse trials, we screened commercial cultivars and 672 U.S. PIs (226 B. juncea and 446 B. rapa) for resistance to Psm with artificial inoculation. Although severity of disease symptoms was significantly different among inoculated accessions, no acceptable levels of resistance were found in any of the more than 400 B. rapa accessions tested. Only two B. juncea accessions (PI 195553 and G 30988) of 226 tested had acceptable levels of resistance that might prove economically useful.
Coevolution of ribosomes and the translational apparatus: The structure and function of eukaryotic ribosomal protein uS7 from yeast, Saccharomyces cerevisiae

High-resolution structures of yeast ribosomes revealed that eukaryotic and bacterial ribosomes share a common ribonucleoprotein core with majority of the changes (addition of rRNA expansion segments and proteins) occurring on the outer shell of the ribosome. The 80S yeast ribosome contains 79 proteins, of which 46 are eukaryote-specific and 34 proteins (15 and 19 in the small and large subunit respectively) are universally conserved. Despite general similarity in sequence and structure, many conserved ribosomal proteins have evolved eukaryote-specific extensions, whose functional significance is largely unknown and/or just beginning to emerge. It has been hypothesized that eukaryote-specific extensions of the conserved ribosomal proteins have evolved to accommodate eukaryote-specific features of the eukaryotic translational apparatus. Yeast, uS7 protein (known as rpS5 in yeast) from the small (40S) ribosomal subunit has evolved an N-terminal extension of ~60 amino acid residues in length. The eukaryote-specific Nterminal extension of rpS5 also forms contacts with N-terminal extension of uS9 (known as rpS16 in yeast).
Comparative Molecular and Structural Characterisation of Chikungunya Virus Isolated Before and After 2006 Epidemics

Background: Chikungunya virus caused incapacitating infection during 2006 epidemics spanning 28 countries. The expansion of the disease and increased virulence resulted in neurological and ocular complications in the affected patients implicating changes in the structural and functional properties of the newly emerging strains of Chikungunya virus. Objective: Hence the study was designed to understand the disparity between two strains isolated before and after 2006 epidemics by both in vitro and in silico approaches with respect to E1 gene. Materials and Methods: Sequencing of E1 gene and phylogenetic analysis of the two strains were carried out followed by the determination of growth pattern. The impact of aminoacid substitutions on the structural properties of E1 protein between the strains of Chikungunya virus was identified by different Bioinformatic tools. Results: Sequencing and Phylogenetic analysis revealed the two strains as Asian (isolated before 2006) and East Central South African (isolated after 2006). ECSA strain produced 1.5 fold log10 titre increased viral production than the Asian strain at the multiplicity of infection 1. Influence of aminoacid difference on the structure of E1 protein between two strains by Bioinformatic analysis Original Research Article Sangeetha et al.; BMRJ, 17(2): 1-11, 2016; Article no.BMRJ. 27880 2 had shown a change in the conformations by the loss of two intermolecular hydrogen bonds in 121 position in Asian strain and electrostatic differences in 211 positions between the two strains was also observed. Conclusion: As the interacting aminoacid 121 and 211 position lies near the fusion loop hence the difference in aminoacid position between the two strains could better influence fusogenicity and stable trimer formation. This forms a preliminary insight on the impact of aminoacid substitutions on the structural properties of E1 protein between the strains of Chikungunya virus and further experimental investigations are warranted.