Miracle-dz/UniFAR-FTUs huggingface dataset:
Short-chain fatty acid content in the hindgut of rats fed various composite foods and commercial dietary fibre fractions from similar sources

The fermentability of indigestible carbohydrates and content of short-chain fatty acids along the hindgut of rats were investigated using plant materials of importance in the Swedish diet (instant potato powder, apples and oat flakes). Results with the composite food products were compared with commercial fibre fractions obtained from similar sources, ie potato fibre, apple pectin and beta-glucan-enriched oat fibre. The materials were incorporated into diets yielding a concentration of 60 or 70 g kg (1) indigestible carbohydrates. The fermentability of indigestible carbohydrates was high with all diets, between 79 and 90%. All substrates except the pure apple pectin generated intermediate to high proportions of butyric acid in the caecum (15-22 vs 8%). The potato products gave high concentrations of butyric acid in the distal colon. The potato powder, ie the diet with the highest content of resistant starch (22g kg(-1)), also gave the highest proportion of butyric acid in the distal colon (19%), which was higher than the proportion in the caecum with the same substrate (15%) (P < 0.005). The composite foods promoted a higher proportion of butyric acid in the distal colon as compared with the commercial fibre fractions (P < 0.05). (C) 2002 Society of Chemical Industry. (Less)
Gyrodactylid biology, transmission and control

Infectious disease in aquaculture is omnipresent, but traditional treatments used against the causative agents often have broad anti-parasitic properties, are not 100 % efficacious, are toxic to humans, fish and the environment, and successful application is challenging. Hence, integrated disease management that combines an understanding of parasite life history and host welfare with treatment is highly recommended. This thesis examined the life history characteristics of a ubiquitous genus of fish ectoparasites, Gyrodactylus species, and tested the efficacy of botanical treatments against gyrodactylids using the guppy (Poecilia reticulata) infected by G. turnbulli or G. bullatarudis as model, with the aim to work towards an integrated management plan for gyrodactylosis in the ornamental fish industry and the hobbyist market. The experiments conducted have shown that (1) gyrodactylids engage in sexual reproduction and on a population level show hybrid fitness and/or inter-strain competition when diverged genotypes are recombined; (2) parasite transmission is mainly driven by direct contact with potential hosts and on dead fish or after detachment gyrodactylids have a window of opportunity to re-attach of over 20 h; (3) extreme habitats provide guppies with a refuge from microbial and gyrodactylid infections in natural populations; (4) anti-parasitic treatment efficacy may be species specific using traditional methods; and (5) salt, garlic, cajuput oil and a combination treatment of the two commercially available treatments Melafix® and Pimafix® are efficacious alternatives for broad anti-parasitic aquarium treatments against gyrodactylids. Due to their efficient reproduction, gyrodactylids are unlikely to be eradicated, as just a single, pregnant worm can trigger a new disease epidemic. However, combining the knowledge on pathogen life history characteristics and host-parasite interactions with effective treatment application will reduce evolutionary pressures on the pathogen and slow its virulence evolution. Overall, this increases the time available for treatment efficacies to be maintained in a manner which corresponds with new drugs being developed as treatment resistance arises.
Identification of response classes from heavy metal‐tolerant soil microbial communities by highly resolved concentration‐dependent screenings in a microfluidic system

One of the most important constituents in soil is the microflora, mainly containing bacteria and fungi with high metabolic versatility and very complex intra‐ and interspecific interactions. Co‐occurrence of several micro‐organism species in soil regulates growth or suppression of single species, either by mutual tolerance or by induction of defence mechanisms, which may result in the release of secondary metabolites for growth suppression of coexisting species. Accumulations of heavy metals in soils can further affect the growth of soil microbial communities; this however is strongly dependent on the capability of micro‐organisms to tolerate heavy metals. Until now, there is no fast and reliable method available to study the growth of microbial communities in highly resolved concentration spaces with environmentally relevant toxic substances such as heavy metals and to identify the tolerance thresholds of micro‐organism communities of selected soils. Here, we present a new methodological approach for the assessment of the growth–response behaviour of soil microbial communities in response to increasing heavy metal concentration (copper) using the droplet‐based micro‐segmented flow technique. Therefore, micro‐organism‐containing soil slurries from contact with metal artefacts from archaeological excavations and from the surface of early copper‐mining areas were studied by separate cultivation in segments in the sub‐μL range and growth, and fluorescence was characterized after cultivation by combined micro‐flow‐through photometry and fluorimetry. Highly resolved dose–response data provided copper tolerance thresholds of the soil communities of the different soils. Concentration‐dependent growth patterns of the micro‐organisms in the segments could be observed and allowed to distinguish response groups with characteristic distribution of photometric and fluorimetric measurement values. It is assumed that these response groups are caused by a sample characteristic growth of metal‐tolerant microbial communities with characteristic critical metal concentrations for growth inhibition. The clear transitions between the groups in small concentration intervals are probably due to sharp transitions between growth and no growth of dominant micro‐organism species at the critical metal concentration. The investigations demonstrate the potential of droplet‐based microfluidic techniques for ultra‐miniaturized ecological studies and its suitability for the assessment of tolerance thresholds of soil microbial communities from heavy metal‐contaminated areas.
K‐Opiate Agonists Inhibit Adenylate Cyclase and Produce Heterologous Desensitization in Rat Spinal Cord

Abstract: The nature of the opiate modulation of adenylate cyclase following acute and chronic agonist exposure has been investigated in rat spinal cord. Using membranes of both adult rat spinal cord and spinal cord‐dorsal root ganglion cocultures, we found that K‐opiate receptors are negatively coupled to adenylate cyclase. The K‐opiate agonists (e.g., U50488) inhibit significantly and dose‐dependently the basal and the forskolin‐stimulated cyclase activities, whereas μ and δ agonists are ineffective. The regulatory action is stereospecific and requires the presence of GTP. EGTA treatment of the plasma membranes abolished the effect of K‐opiate agonists on the basal cyclase activity, and this inhibitory effect could not be restored by subsequent addition of Ca2+. The EGTA treatment did not affect the K agonist inhibition of the forolin‐stimulated cyclase. The results also show that following chronic exposure of cultured cells to etorphine or U50488, there is a loss of K agonist inhibition of the cyclase. Moreover, this desensitization process appears to be heterologous, because α2‐adrenergic agonists (e.g., clonidine or norepinephrine) and the muscarinic agonist (carbachol) exhibited significantly lower potency for inhibiting cyclase activity when compared to untreated cultures. This pattern of heterologous desensitization suggests that chronic exposure to K opiates leads to alterations in postreceptor regulatory components, possibly GTP‐binding proteins.
Families and genera of Cape Verdean spiders in comparison to those of the Canary Islands

of the 25 families, 48 of the 75 genera and 25 of the 116 species of spiders, present on the Cape Verde Islands also occur on the Canary Islands. 15 of these species are transgressing, 6 are cosmopolitan and 4 are of Makaronesian origin. There is no more than one species common in those genera occurring on both archipelagos. The Cape Verde Islands are the most southern distribution for 9 species living on the Canary Islands.
The Effect of Flower Maturity and Harvest Timing on Floral Extract fromBoronia megastigma(Nees)

Development of floral organs during maturation of flower buds into fully open boronia flowers is described. The petals and functional anthers attain their maximum size prior to the non-functional anthers and the stigma. Organoleptic properties of the floral extract change with successive stages of bud development. The concentrations of extract and volatiles in the extract (% by f. wt) increase as buds mature, the extract concentration being highest in large buds and open flowers and the concentration of volatile compounds being highest in open flowers. The rate of flower and extract development was measured. Yields of flower material and floral extract per plant, and the concentration of total volatiles including β-ionone reach maximum levels when 70% of flowers have reached anthesis. All measured factors decline after this point, except extract concentration (% of f. and d. wt) which is maintained up to 83% open flowers.
ECOSYSTEM CONTROL OVER TEMPERATURE AND ENERGY FLUX IN NORTHERN PEATLANDS

Large-scale changes in climate may have many unexpected effects on ecosystems, given the importance of climate as a control over almost all ecosystem attributes and their many internal feedbacks. In particular, the interactions among energy flux, plant dynamics, and soil carbon and nutrient cycling are poorly known. In this study, we examined biotic controls over soil temperature and evapotranspiration (ET) in a climate change experiment in two peatlands, a bog and a fen. Bogs are isolated from groundwater inputs (i.e., ombrogenous) and are acidic, whereas fens receive groundwater inputs (i.e., minerogenous) and are more alkaline. They also have many associated differences in soil chemistry, nutrient availability, and plant communities. We removed 27 intact peat monoliths each from a bog and a fen in northern Minnesota to construct a large mesocosm facility that allows for direct manipulation of climatic variables in a replicated experimental design. The treatment design was a fully crossed factorial with.
Genetic variability in the brazilian criollo horse breed

Allelic frequencies of 7 blood groups and 8 protein systems were determined in 6 herds of Criollo horse breed raised in Rio Grande do Sul, Brazil. Analysis of these frequencies showed a significant isolation component (Fst = 0.0866; p<0.01) and construction of dendogram using Nei´s D confirmed this difference among the 6 herds. The highest values measuring genetic variability on 15 blood types were average heterozygosity: 0.4631; total number of alleles: 87 and probability of exclusion: 98%. When all herds were considered together, the inbreeding level (Fis) was zero. These results indicate that the Criollo horses have a large genetic variability.
Discovering MicroRNAs and Their Targets in Plants

MicroRNAs (miRNAs) are a subset of endogenous approximate 22 nucleotide (nt), small non-coding regulatory RNA molecules that regulate gene expression post-transcriptionally by mediating mRNA degradation or translational repression in a sequence specific manner. Plant miRNA research gained momentum, 2002 onwards, which was accompanied by the discovery of plant proteins involved in miRNA biogenesis. Progress in genomic research of different plant species may open the door for discovering novel miRNAs and their characteristics. With the development and availability of experimental technologies and computational approaches, the field of miRNA biology has advanced tremendously over the last decade. This paper aims to introduce major computational approaches in the identification of plant miRNAs, including conservation based search, de novo prediction and mining in deep sequencing data. Computational tools for identification of miRNAs target is another intriguing perspective that has been examined in this review. All these approaches have certain advantages and disadvantages, which are reviewed in the present survey. Furthermore, in the present survey, we also present many experimental modalities such as Degradome sequencing, Immunoprecipitation of RISC components and their limitations for miRNAs targets identification. At the end, we also present the outlook for future directions in the development and improvement of plant miRNA discovery methods.
A note on common minke whale (Balaenoptera acutorostrata) diets in the Norwegian Sea and the North Sea

Visual observations and quantitative samples of forestomach contents were made of minke whales caught in the Norwegian Sea (15 visual observations in 1999, 8 in 2000 and 1 stomach sample) and North Sea (15 visual observations and 7 stomach samples, all from 1999). Prey species were identified, and from the forestomach samples, each prey’s relative contribution by weight to the diet was calculated. In the Norwegian Sea, the diet was dominated by Norwegian spring-spawning herring (100%). This was consistent with the large and dominant abundance of herring in the area. Observations and forestomach samples from the North Sea indicated a more varied diet, with sandeel (Ammodytes spp.) contributing 86.7% to the diet by weight, followed by mackerel (9.3%), whiting (2.4%), herring (1.1%) and Norway pout (0.5%). Haddock was observed in one stomach, but was not found in any of the samples. Sandeel occurred in all observed and four of the sampled stomachs. The domination of pelagic species in the diet strongly indicates pelagic feeding behaviour in both areas.
Current methods of laboratory diagnosis of Chlamydia trachomatis infections

Infections caused by Chlamydia trachomatis are probably the most common sexually transmitted diseases in the United States. Commonly unrecognized and often inadequately treated, chlamydial infections can ascend the reproductive tract and cause pelvic inflammatory disease, which often results in the devastating consequences of infertility, ectopic pregnancy, or chronic pelvic pain. C. trachomatis infections are also known to increase the risk for human immunodeficiency virus infection. The obligate intracellular life cycle of C. trachomatis has traditionally required laboratory diagnostic tests that are technically demanding, labor-intensive, expensive, and difficult to access. In spite of these historical challenges, however, laboratory diagnosis of C. trachomatis has been a rapidly advancing area in which there is presently a wide array of commercial diagnostic technologies, costs, manufacturers. This review describes and compares the diagnostic methods for C. trachomatis infection that are currently approved for use in the United States, including the newest DNA amplification technologies which are yet to be licensed for commercial use. Issues to consider in selecting a test for purposes of screening versus diagnosis based on prevalence, performance, legal, social, and cost issues are also discussed.
Determination of viral load and integration status of HPV 16 in normal and LSIL exfoliated cervical cells

Integration of human papillomavirus (HPV) has, until recently, been a frequent but late event in cervical carcinogenesis. The temporal view has, however, been challenged lately as integrated forms of HPV have been detected even in normal and preneoplastic lesions. Our objective was to describe HPV 16 load and physical state in a series of 220 normal and low grade cervical samples. We used quantitative real-time PCR, Taqman method, targeting E6, E2 and B-globin to calculate the HPV 16 load and the E6/E2 ratio in each sample. An E6/E2 ratio of 1.2 was used as a surrogate marker of integration. The site of integration was determined by restriction site PCR. Results show that the average viral load was 57.5±324.6 copies of DNA per cell, while E6/E2 ratio identified 9 samples with integrants. These integrants underwent amplification by restriction site PCR, followed by sequencing and nucleotide blast to identify the human-viral junctions. In conclusion, although it was possible to identify viral-host junctions with the integration positive control, that is, the SiHa cell line, the exfoliated cells of normal and low grade cervical lesions were negative for integration site by RS-PCR. HPV-16 is seldom integrated in specimens from young patients.
The molecular analysis of the effects of lumichrome as a plant growth promoting substance

The response of Lotus japonicus roots to lumichrome on gene expression, protein and metabolite levels was evaluated. On the gene expression level, DNA microarrays revealed increases in the gene expression of the functional categories stress and defence, signaling and RNA regulation of transcription. Remarkably, many of the genes in the categories signaling and RNA regulation of transcription are also implicated in abiotic and biotic stress responses, indicating that lumichrome is perceived as a stress signal. The proteomic analysis resulted in the identification of five proteins that were present in lower abundance in lumichrome treated roots. A more targeted analysis of GS1 and GAPDH was performed to confirm the relevance and importance in the lumichrome mediated growth promotion. Contradictory to the proteomic results, northern blot analysis indicated an increase in transcript levels of GS1 and GAPDH. The microarray data confirmed the result, however, only for GS1. Enzyme activities for both GS1 and GAPDH showed no significant difference between lumichrome treated and untreated roots. Moreover, western blot analysis for GS1 could not detect significant differences in protein levels. Therefore, one can conclude that GAPDH seem to be under posttranslational modification, however, further investigation is needed to confirm this statement. With GS1, further analysis is needed, as multiple isoenzymes exist for GS1 and the protein analyzed with 2-DE could be one of the isoenzymes showing differential expression. However, both seem to play a pivotal role in lumichrome mediated growth promotion although a complex mechanism appears to be at work. In treated plants, most of the metabolite changes occurred in the amino acid pool and point to nitrogen deficiency and oxidative stress.
Conservation in Conflict: the Tale of Two Endangered Species

Abstract: With its umbrella of provisions, the U.S. Endangered Species Act ( ESA ) provides critical protection to threatened or endangered wildlife. It provides minimal guidance, however, on identifying taxa worthy of conservation, lacks guidelines for resolving endangered species conflicts, and subsequent recovery programs often focus on the species rather than the ecosystem. These deficiencies are exemplified by the recovery program for the San Clemente Loggerhead Shrike ( Lanius ludovicianus mearnsi ) and the recent proposed rule to grant federal protection to one of its predators, the island fox ( Urocyon littoralis ). Recovery actions that have included euthanasia of foxes have likely contributed to a 40–60% decline in the population size of the San Clemente Island fox ( U. l. clementae ), a subspecies listed by the state of California as threatened. The U.S. Fish and Wildlife Service proposes to list four other subspecies of the island fox as endangered but excludes the San Clemente Island fox and the sixth and last subspecies, the San Nicolas Island fox ( U. l. dickeyi ), ignoring their evolutionary distinctness and the recent decline in population size of U. l. clementae. Using published morphological and genetic information, we show that the shrike's current taxonomic and legal status should be reevaluated. We also reexamine the current recovery program for the shrike and conclude that the implementation of the ESA's provisions to protect the shrike was species‐centric. The shrike recovery program is primarily centered on two approaches: the release of captive‐bred shrikes and control of native and non‐native predators. The predator control program has contributed to the endangerment of the distinct San Clemente Island fox. Given that five of the six fox subspecies face extirpation, the proposed rule to list only four of the six as endangered is inadequate. This endangered‐species conflict might have been avoided through a more balanced ecosystem approach that considers the ecological role of all native taxa and strives to enhance habitats critical to both the shrike and the fox.
PALEOBOTANICAL EVIDENCE AND MOLECULAR DATA IN RECONSTRUCTING THE HISTORICAL PHYTOGEOGRAPHY OF RHIZOPHORACEAE1

Abstract The fossil record of the Rhizophoraceae includes numerous questionable identifications from strata of unconfirmed age, together with others representing clear evidence of the family in deposits whose age is well constrained by independent or multiple lines of evidence. Bruguiera or the Bruguiera lineage, and Ceriops are known from the early Eocene, Kandelia from the middle Eocene, and Rhizophora from the late Eocene. Combretocarpus is likely present by the middle Miocene, but it belongs to a family (Anisophylleaceae) earlier placed in the Rhizophoraceae that is now considered unrelated to that family. Rhizophora, as a genus, has existed essentially uninterruptedly in the Caribbean region since the late Eocene, but cooling events at ca. 15–14 Ma, ca. 3.4 Ma, and ca. 1.6 Ma, and the subsequent 18 to 20 glacial intervals provide a mechanism for development of the cold(er) tolerant populations toward the northern part of its range in the New World. In reconstructing the biogeographic history of Rhizophora in the Caribbean region, it is worthwhile noting that molecular-defined lineages (with little morphological or palynological variation) may have been introduced and gone extinct on multiple occasions. This allows for variation in molecular patterns and apparent stasis in the fossil record—a possibility not widely considered in the literature. The most recent molecular-defined common ancestor to existing populations is estimated to have arrived in the New World ca. 11 Ma, using an origin in the Paleocene (ca. 60 Ma) as the basis for calculation.
Time lags for xylem and stem diameter variations in a Scots pine tree

Diameter variations in the xylem and whole stem (i.e. over bark) stem of a Scots pine ( Pinus sylvestris L.) tree were measured at four heights over a 23 d period at 5 min intervals. Cross-correlation analysis was used to calculate time lags between the measurements. Xylem diameter measurements at the different heights had time lags varying from 10 to 50 min, measurements at the lower heights lagging behind the most. This result was in good agreement with the cohesion theory of transpiration. For the whole stem diameter measurements, the treetop lagged behind all other heights and the shortest lags were midway along the stem. Changes in whole stem diameter always lagged behind those of xylem stem diameter (30‐110 min), and at all heights. The considerable differences in the behaviour of xylem and whole stem diameter support the Munch hypothesis of phloem flow. Time lags calculated separately for the shrinkage (morning) and swelling (afternoon) periods indicated shorter time lags during the swelling periods. The non-destructive methods used show promise in the simultaneous study of flow dynamics of xylem and phloem in trees.