Miracle-dz/UniFAR-FTUs huggingface dataset:
A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision

Abstract Mitochondrial genomes provide a promising new tool for understanding deep‐level insect phylogenetics, but have yet to be evaluated for their ability to resolve intraordinal relationships. We tested the utility of mitochondrial genome data for the resolution of relationships within Diptera, the insect order for which the most data are available. We sequenced an additional three genomes, from a syrphid, nemestrinid and tabanid, representing three additional dipteran clades, ‘aschiza’, non‐heteroneuran muscomorpha and ‘basal brachyceran’, respectively. We assessed the influence of optimality criteria, gene inclusion/exclusion, data recoding and partitioning strategies on topology and nodal support within Diptera. Our consensus phylogeny of Diptera was largely consistent with previous phylogenetic hypotheses of the order, except that we did not recover a monophyletic Muscomorpha (Nesmestrinidae grouped with Tabanidae) or Acalyptratae (Drosophilidae grouped with Calliphoridae). The results were very robust to optimality criteria, as parsimony, likelihood and Bayesian approaches yielded very similar topologies, although nodal support varied. The addition of ribosomal and transfer RNA genes to the protein coding genes traditionally used in mitochondrial genome phylogenies improved the resolution and support, contrary to previous suggestions that these genes would evolve too quickly or prove too difficult to align to provide phylogenetic signal at deep nodes. Strategies to recode data, aimed at reducing homoplasy, resulted in a decrease in tree resolution and branch support. Bayesian analyses were highly sensitive to partitioning strategy: biologically realistic partitions into codon groups produced the best results. The implications of this study for dipteran systematics and the effective approaches to using mitochondrial genome data are discussed. Mitochondrial genomes resolve intraordinal relationships within Diptera accurately over very wide time ranges (1–200 million years ago) and genetic distances, suggesting that this may be an excellent data source for deep‐level studies within other, less studied, insect orders.
Effect of the Nematodes Acrobeloides Sp. and Mesodiplogaster Lheritieri on Substrate Utilization and Nitrogen and Phosphorous Mineralization in Soil

Release of nutrients by bacterial—feeding nematodes may result in increased nutrient availability for plants. Effects of two species of bacterial—feeding nematodes on N and P mineralization and C—substrate utilization were examined in soil microcosms. Both nematodes increased the rate of 14C—labelled glucose—C utilization and N and P mineralization after 10d. However, after 65 d incubation, soluble C, Pi and NH4+—N were similar in grazed and ungrazed systems. The bacterial grazers, although not directly affecting total decomposition, act to maintain the dynamic nature of the nutrient cycles. See full-text article at JSTOR
A molecular membrane model of sperm capacitation and the acrosome reaction of mammalian spermatozoa

The abundance of data pertaining to the metabolism of lipids in relation to mammalian fertilization has warranted an effort to assemble a molecular membrane model for the comprehensive visualization of the biochemical events involved in sperm capacitation and the acrosome reaction. Derived both from earlier models as well as from current concepts, our membrane model depicts a lipid bilayer assembly of space-filling molecular models of sterols and phospholipids in dynamic equilibrium with peripheral and integral membrane proteins. A novel feature is the possibility of visualizing individual lipid molecules such as phosphatidylcholine, phosphatidylethanolamine, lysophospholipids, fatty acids, and free or esterified cholesterol. The model illustrates enzymatic reactions which are believed to regulate the permeability and integrity of the plasma membrane overlying the acrosome during interactions between the male gamete and capacitation factors present in fluids of the female genital tract. The use of radioactive lipids as molecular probes for monitoring the metabolism of cholesterol and phosphatidylcholine revealed the presence of (1) steroid sulfatase in hamster cumulus cells, (2) lecithin: cholesterol acyltransferase in human follicular fluid, (3) phospholipase A2, and (4) lysophospholipase in human spermatozoa. These enzymatic reactions can be integrated into a pathway that provides a link between the concepts of lysophospholipid accumulation in the sperm membranes and alteration of the cholesterol/phospholipid ratio as factors involved in the preparation of the membranes for the acrosome reaction. Capacitation is viewed as a reversible phenomenon which, upon completion, results in a decrease in negative surface charge, an efflux of membrane cholesterol, and an influx of calcium between the plasma and outer acrosomal membranes. Triggered by the entry of calcium, the acrosome reaction involves phospholipase A2 activation followed by a transient accumulation of unsaturated fatty acids and lysophospholipids implicated in membrane fusion which occurs during the formation of membrane vesicles in spermatozoa undergoing the acrosome reaction.
Diet‐tissue fractionation of δ15N by consumers from streams and rivers

Variation in the diet‐tissue fractionation of stable nitrogen isotopes (Δ15N) is a major source of uncertainty in mixing model outputs and the calculation of trophic level in food web studies in aquatic systems. Using δ15N and δ13C of algae and consumers collected from a broad range of streams and rivers in Australia and New Guinea, we calculated Δ15N using a gradient approach, and compared these estimates with those from the literature. Riverine invertebrates and fishes from this region have δ15N diet‐tissue fractionation at the low end of the range of values reported for literature summaries, but different trophic groups had different Δ15N estimates. Source‐consumer regressions based on δ13C had lower slope estimates and lower R2 values compared with those based on δ15N. This implies that although consumers on average obtain a portion of their organic carbon from higher plants, they derive most of their organic nitrogen from N‐rich algae. Use of appropriate Δ15N for riverine consumers will lead to more satisfactory results with isotope mixing models, and the uncertainty associated with Δ15N estimates can be incorporated in the latest iterations of these models that are probabilistic rather than deterministic.
Resistance to nematode parasites in Merino sheep: sources of genetic variation

Merino sheep representing a range of bloodlines in resource flocks located across Australia were tested for resistance to gastro-intestinal nematodes. These flocks included the JB Pye Flock (Camden, NSW), Katanning Base Flock (Katanning, WA), Turretfield Merino Resource Flock (Rosedale, SA), CSIRO Finewool Flock (Armidale, NSW), and the Trangie D Flock (Trangie, NSW). Faecal egg count (FEC) was used to measure relative resistance of sheep to nematode parasites after either natural or artificial infection with Haemonchus contortus and Trichostrongylus colubriformis. Differences in FEC' ' 33 between strains and between and within bloodlines were examined and the heritability of this trait was estimated. A low proportion of the total variation in parasite resistance could be attributed to strain and bloodline effects (1 and 3.5%, respectively) after either natural or artificial infection. The major source of genetic variation was found within bloodlines (22.2% of total variation), with individual sires showing a wide range in parasite resistance. Paternal half-sib heritability estimates for FEC''~~ were significant (P < 0.05) in 9 of the 11 analyses and ranged from 0.07 to 0.42, with a weighted average of 0.22. The influence of the environmental effects of sex, age of dam, birth-rearing rank, and day of birth were also investigated, and were found to be only occasionally significant, accounting for a small proportion (0.3-2.2%) of variation. Management group effects both prior to and at the time of measurement were often significant, and accounted for 2.2-19.4% of variation in FEC. Correction of FEC for effects other than management group would seem to add little to precision of selection. These results have demonstrated that significant genetic variation for nematode parasite resistance exists within a wide range of Merino bloodlines, and within-flock selection of resistant sires appears to be an effective method of improving this trait in Merino sheep. Additional keywords: heritability, faecal egg count, parasite resistance, variance components.
Ant species distribution along a topographic gradient in a "terra-firme" forest reserve in Central Amazonia.

Na Amazonia, variacoes topograficas em ecossistemas de terra-firme sao variaveis comuns que afetam a distribuicao de invertebrados terrestres. O objetivo deste trabalho foi avaliar os efeitos do conteudo de argila no solo e da inclinacao do terreno na distribuicao de especies de formigas em uma area de 25 km2 que cobre a variacao topografica natural. Usando tres metodos de coleta complementares (iscas de sardinha, armadilhas de fosso e amostras de serapilheira extraidas de sacos de Winkler), foram coletadas 300 subamostras de cada metodo em 30 parcelas distribuidas em uma floresta tropical umida na Reserva Ducke (Manaus, AM). Foram registrados 26.814 individuos em 11 subfamilias, 54 generos, 85 especies e 152 morfoespecies (Pheidole representou 37% das morfoespecies). O genero Eurhopalothrix foi registrado pela primeira vez nesta reserva. O numero de especies nao foi correlacionado com a inclinacao do terreno ou o conteudo de argila, exceto para especies na serapilheira. No entanto, a Analise das Coordenadas Principais indicou que a composicao de especies das armadilhas e da serapilheira esteve correlacionada com o conteudo de argila. Aproximadamente metade das especies foi encontrada somente nos baixios ou nos platos, sugerindo que a maioria e especialista do habitat. Na Amazonia Central, a textura do solo esta geralmente correlacionada com a estrutura da vegetacao e o teor de umidade, criando micro-habitats heterogeneos que provavelmente contribuiram para as diferencas observadas na estrutura da comunidade de formigas.
Chemistry of a colour test for abscisic acid

Abscisic acid and its methyl ester are converted by acid-catalysed dehydration into neutral products, one of which has been identified as an unsaturated γ-lactone. It gives an intense violet-red colour with alkalis, which fades as the lactone is hydrolysed. This reaction is a useful qualitative test for abscisic acid.
Fitness consequences of the timing of metamorphosis in a freshwater crustacean

Metamorphosis is a common life-cycle transition in organisms as diverse as amphibians, insects, fishes and crustaceans, and the timing of this transition often affects an individual's fitness. Here, we measured age and size at metamorphosis in laboratory-reared individuals of the freshwater copepod, Diaptomus leptopus, and then followed individuals over their entire life cycle to assess the fitness consequences of variation in age and size at metamorphosis. In 3 separate experiments, individuals were raised in different food conditions: low food (0.2 μg C/ml) switched to high food (0.7 μg C/ml), or high food switched to low food, at several different larval and juvenile stages. Control individuals were reared on high or low food concentrations over their entire life cycles. For each individual, we measured age and size at metamorphosis and age and size at maturity; for females, we also measured total lifetime egg production, longevity, and calculated a composite fitness measure, λ. Statistical analyses showed no significant effects of age or size at metamorphosis on these same traits measured at maturity, or on the fitness components we estimated. The first individuals to mature had the highest total egg production and individual fitness; differences in body size at maturation explained none of the variation observed in fitness components. Our results show that metamorphosis was uncoupled from maturity and from fitness components by growth and development achieved during the juvenile phase of the life cycle, and support the conclusion that fitness consequences of metamorphosis depend fundamentally on the organization of an organism's life cycle. They also suggest that body size plays a different life-history role in these organisms than is recognized in most poikilotherms, and suggest the hypothesis, based on laboratory experiments, that selection may act primarily on juvenile developmental rates in field populations.
Mapping Correlates of Parasitism in Wild South African Vervet Monkeys (Chlorocebus aethiops)

A growing focus of nonhuman primate conservation and management planning concerns factors affecting the dynamics of parasite infection and disease transmission. Here, we examine the effects of anthropogenic and environmental components of the landscape on the prevalence, richness, and species diversity of gastrointestinal parasites in wild-caught vervet monkeys (Chlorocebus aethiops) in South Africa. Nematodes of the genus Trichuris and the family Strongylidae and protists of the subclass Coccidia were present in 55.13% of sampled animals (n = 43). Parasitological, geographical, demographic and climatic correlates of infection were assessed in a geographical information systems (GIS) platform. The findings of this study suggest that parasitism in South African vervets may be better predicted by environmental factors than by degree of anthropogenic contact. This research represents one of the first surveys of parasitic infection in a wild monkey species in southern Africa.
Controlled-release components of PZP contraceptive vaccine extend duration of infertility

Successful immunocontraception of wildlife relying on repeated access to individuals for boosters has highlighted the need to incorporate primer and booster immunisations into one injection. We have investigated use of controlled-release polymers (lactide–glycolide) in small pellets to provide delayed in vivo delivery of booster porcine zona pellucida (PZP) antigen and adjuvant. This report reviews pellet-making methodology, in vitro testing of controlled-release pellets and in vivo effects of controlled-release PZP vaccine. We assessed 3 different manufacturing approaches for producing reliable, cost-effective pellets: (1) polymer melting and extrusion; (2) solvent evaporation from polymer solution; and (3) punch and die polymer moulding. In vitro testing of release patterns of controlled-release formulations, towards development of a 3-year duration vaccine, provided estimates for in vivo use of pellet preparations. These in vitro studies demonstrated protein release delay up to 22 months using 100% l-lactide or polycaprolactone polymers. For in vivo tests, pellets (1-, 3-, and 12-month release delay) serving as boosters were administered intramuscularly with PZP/adjuvant liquid primer to wild horses (Equus caballus), white-tailed deer (Odocoileus virginanus) and African elephants (Loxodonta africana). Horse field studies assessed fertility via offspring counts and/or faecal-hormone pregnancy testing. Treatment decreased fertility 5.3–9.3-fold in Year 1 and 3.6-fold in Year 2. In preliminary testing in deer, offspring counts revealed treatment-associated fertility reduction of 7.1-fold Year 1 and 3.3-fold Year 2. In elephants, treatment elevated anti-PZP titres 4.5–6.9-fold from pretreatment (no fertility data).
SELDI Based Proteomic Determination of Hepatic Biomarkers in Mouse Serum Following Acetaminophen Administration

Drug induced toxicities account for nearly half of the cases of acute liver failure in adults over age 50 in the US. Acetaminophen (APAP) is a commonly used non-prescription drug that can be purchased in drug stores and supermarkets. Cases of unintentional APAP overdose and associated hepatotoxicity have been reported to the FDA. Early detection of hepatotoxicity caused by APAP is of great interest to both the scientific and public communities. Therefore, in this study SELDI based analysis of mouse serum following APAP administration was conducted to demonstrate the feasibility of identifying hepatic toxicity biomarkers from a readily available body fluid. Late hepatotoxicity caused by APAP was detected by SELDI. Furthermore, early stage hepatotoxicity caused by APAP that was not detected pathologically was clearly discernable using SELDI. Our results suggest that SELDI analysis can be used for early detection of hepatotoxicity based on the expression pattern of the biomarker peaks.
THE USE OF A SELECTIVE MEDIUM FOR THE ENUMERATION OF LACTOBACILLI IN CHEDDAR CHEESE

SUMMARY: The use of a selective solid medium for counting lactobacilli in Cheddar cheese is described. It has proved useful for this purpose, especially in the early period of ripening when large numbers of streptococci render other methods impracticable. The medium, in a semisolid form, is more sensitive for the detection of heterofermentation in lactobacilli than media previously available. The possibility of using it to count heterofermentative lactobacilli and leuconostocs is discussed.
HISTOCHEMICAL AND ELECTRON MICROSCOPIC OBSERVATIONS OF GLYCOGEN SYNTHESIZED FROM GLUCOSE-1-PHOSPHATE BY PHOSPHORYLASE AND BRANCHING ENZYME IN HUMAN MUSCLE

Polysaccharides synthesized histochemicaily from glucose-i -phosphate by amylophosphorylase alone or by both phosphorylase and branching enzyme in human skeletal muscle fibers were observed with the electron microscope. Histochemically the newly formed polysaccharides were stained blue in smaller muscle fibers and violet or red purple in larger ones with the iodine reaction. Low-density, amorphous areas contaming denser cloudy material with a few small particles were noted in the cytoplasmic matrix to the exclusion of all other components or organelles. It was considered that phos )horylase and branching enzyme might be localized in these.
Improved bioavailability of orally delivered peptides and polypeptides in teleost fish

Summary A gonadoliberin analogue (GnRHa) whose biological role is the stimulation of gonadotropin (GTH II) secretion, has been encapsulated together with intestinal absorption enhancers and proteolytic enzyme inhibitors. The capsules have been coated to prevent their solubilization at acid pH in the stomach. After oral delivery of the capsules by forced-feeding, high GnRHa intestinal absorption and high bioavailability in the blood results. GTH II secretion was stimulated in a dose-dependent manner by the orally delivered GnRHa in three species having different digestive tract structures and different feeding habits: the rainbow trout, the common carp and the African catfish. In addition, the oral delivery of GnRHa also results in the induction of ovulation in all three species at doses similar to those usually used to induce spawning in these species. There was no competition of nutrient given together with the microcapsules on GnRHa absorption. From these results, it becomes possible to develop special diets containing microencapsulated bioactive peptides for use in therapy or to modify nonvital functions in fish. In the present case, an orally-induced ovulation treatment will be developed.
Effects of beech bark disease on the growth of American beech (Fagus grandifolia).

We studied radial growth reduction in American beech (Fagusgrandifolia Ehrh.) in relation to the level of defect induced by beech bark disease, in second-growth and old-growth northern hardwoods stands in New Hampshire. In the second-growth stand at Moose Mountain (n = 243 trees), 1989–1990 radial growth declined significantly with increasing severity of external symptoms. The severity of external symptoms increased significantly with DBH. To examine temporal trends, internal defect induced by the disease was quantified as the percentage of growth sheath cankered in each year, by cross-sectioning a subsample of 40 trees. Internal defect first appeared in 1950, increased through 1969, then declined until a major pulse of infection in the period 1983–1987. Sectioned trees were divided into infection classes based on a cumulative measure of internal defect. Growth of severely infected trees first fell below that of uninfected trees in 1965, and was consistently lower after 1972. The growth ratio of severely .
The GroE chaperonin machine is a major modulator of the CIRCE heat shock regulon of Bacillus subtilis

Class I heat‐inducible genes in Bacillus subtilis consist of the heptacistronic dnaK and the bicistronic groE operon and form the CIRCE regulon. Both operons are negatively regulated at the level of transcription by the HrcA repressor interacting with its operator, the CIRCE element. Here, we demonstrate that the DnaK chaperone machine is not involved in the regulation of HrcA and that the GroE chaperonin exerts a negative effect in the post‐transcriptional control of HrcA. When expression of the groE operon was turned off, the dnaK operon was significantly activated and large amounts of apparently inactive HrcA repressor were produced. Overproduction of GroEL, on the other hand, resulted in decreased expression of the dnaK operon. Introduction of the hrcA gene and its operator into Escherichia coli was sufficient to elicit a transient heat shock response, indicating that no additional Bacillus‐specific gene(s) was needed. As in B.subtilis, the groEL gene of E.coli negatively influenced the activity of HrcA. HrcA could be overproduced in E.coli, but formed inclusion bodies which could be dissolved in 8 M urea. Upon removal of urea, HrcA had a strong tendency to aggregate, but aggregation could be suppressed significantly by the addition of GroEL. Purified HrcA repressor was able specifically to retard a DNA fragment containing the CIRCE element, and the amount of retarded DNA was increased significantly in the presence of GroEL. These results suggest that the GroE chaperonin machine modulates the activity of the HrcA repressor and therefore point to a novel function of GroE as a modulator of the heat shock response.
Studies on the Laccase of Lentinus edodes: Specificity, Localization and Association with the Development of Fruiting Bodies

The phenol oxidases from mature fruiting bodies of Lentinus edodes (Berk.) Sing. , a commercially cultivated mushroom, were studied. The major phenol oxidase was a laccase with a pH optimum near 4.0 and an apparent molecular weight of 100000. Catechol oxidase and tyrosinase were also present. The laccase investigated was primarily extracellular; the highest activity was in the pigmented rind of the pileus and in the stipe. Increased laccase activity was associated with rapid growth of non-pigmented aerial mycelium and formation of pigmented primordia and fruiting bodies. Possible functions of the laccase and its regulation during the development of fruiting bodies are discussed.