Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative characterisation of reef fish diversity among nearshore habitats in a northeastern New Zealand marine reserve

Abstract The influence of habitat type upon reef fish assemblage structures has been extensively reported, but there is still a need to quantitatively demonstrate the factors driving reef fish assemblages within and among habitats. This mensurative study examined diversity and community composition of reef fish assemblages between five habitats (shallow kelp, deep kelp, sand, algal turf, and sponge fiats) within the Cape Rodney‐Okakari Point Marine Reserve, northeastern New Zealand. Two contrasting sampling techniques, point count and timed search were used to quantify a range of species with different life history strategies and characteristics. Diversity generally decreased from kelp to sand habitats. Different habitat types displayed significantly different assemblages irrespective of the sampling technique used, as tested using two different multivariate techniques: constrained canonical analysis of principal coordinates and analysis of similarities (CAP, ANOSIM). Differences in depth between defined habitat types explained a significant proportion of variability in fish assemblage data (17% and 28% for the point count and timed search data, respectively), although a large proportion of variability was unexplained. A core group of species were found to be best discriminators among habitats, including Meuschenia scaber, Parapercis colias, Upeneichthys lineatus, Cheilodactylus spectabilis, Notolabrus celidotus, Notoclinops segmentatus, Forsterygion lapillum, and F. varium. Sand habitat was characterised by a general absence of species. This study examined analytical methodology for characterising reef fish assemblages using existing statistical procedures and demonstrates the ability to detect significant differences in fish communities among different nearshore habitats along the northeastern coast of New Zealand. Further monitoring and measuring of other environmental parameters would allow the creation of an explanatory model for relative fish community abundances for the northeastern coast of New Zealand.
Morphologic and Cytochemical Characteristics of Asian Yellow Pond Turtle (Ocadia sinensis) Blood Cells and their Hematologic and Plasma Biochemical Reference Values

Abstract Hematologic analyses are useful for the monitoring of animal health and diseases and for the differentiation of physiologic processes for clinicians and conservationists. In order to establish hematology reference values for the Asian yellow pond turtle (Ocadia sinensis) and to produce an accurate baseline of clinical laboratory data for O. sinensis with regard to sex and season, 50 (24 males and 26 females) adult captive individuals of O. sinensis were studied. Blood samples from the jugular veins of the turtles were collected in January, April, June, and November. Data were analyzed using repeated measures analysis of variance for significant (P < 0.05) variation by sex, season, and the interaction between sex and season. Significant sex differences were observed for the parameters of packed cell volume, eosinophil count, heterophils and monocytes ratio, total protein, albumin, uric acid, aspartate aminotransferase, alanine aminotransferase, triglycerides, cholesterol, and alkaline phosphatase. Marked seasonal variation was noted in all parameters except mean cell hemoglobin, monocytes and heterophils ratio, and creatinine. Differences between sexes and seasons were primarily associated with the reproductive cycle. Heterophils had a strong positive reaction and eosinophils had a moderate positive reaction to benzidine peroxidase stain. Thrombocytes had a positive reaction to periodic acid-Schiff stain. Surface morphologic study using scanning electron microscopy of blood cells showed that white blood cells of O. sinensis had no distinctive surface characteristics.
Microfibril Angle Distribution of Poplar Tension Wood

Tension wood of poplar (Populus nigra) branches was studied by lightand electron microscopy. The characteristic features of tension wood such as wider growth rings, reduced vessel density and higher gross density were confirmed by our results. Based on a novel combination of transmission electron microscopy (TEM) imaging and image analysis, involving Fourier transformation, the orientation of cellulose microfibrils in the S2- and G-layer was determined. Within the G-layer microfibril angle (MFA) was parallel to the growth axis (0°). However, in the S2 it was 13° in tension wood fibres and 4° in normal wood fibres. With the exception of the relatively low fibril angle in the S2 of tension wood fibres (13°) the results are in good agreement with those of the literature.
Construction and Expression in Tobacco of a β-Glucuronidase (GUS) Reporter Gene Containing an Intron Within the Coding Sequence

An Intron-GUS reporter gene which contains a modified intron of the castor bean catalase gene within the N-terminal part of the β-glucuronidase (GUS) coding sequence was constructed. When the Intron-GUS reporter gene placed downstream of the cauliflower mosaic virus (CaMV) 35S promoter (35S-Intron-GUS) was introduced into protoplasts of tobacco suspension-cultured cells by electroporation, expression of GUS activity was observed suggesting splicing of the intron occured in tobacco cells
Benthic diatoms of the Vistula River estuary (Northern Poland): Seasonality, substrata preferences, and the influence of water chemistry

Seasonal studies of water bodies in separate branches of the Vistula River estuary in Northern Poland were conducted over 30 months from May 2005 to October 2007. Diatom samples were collected from different substrata from two sites located in the river mouth, which has physical characteristics as a result of a complex interplay of natural and human influences that have taken place over the last 100+ years. The diatom flora growing on hard surfaces near the river banks such as sand, muddy sand, rocks, macroscopic green algae and/or vascular aquatic plants was recorded. All diatom taxa collected were distinguished based on their morphological features using light (LM) and scanning electron microscopy (SEM). A total of 187 species belonging to 61 genera were identified. A canonical correspondence analysis indicated that the diatom assemblages were definitely associated with salinity as well as nutrient concentrations and substratum type. During the study, malformations of diatom valves were observed in 48% of the microphytobenthos samples. Abnormal outline morphology and ornamentation deformities in several individuals of nine different species were recorded, which were mainly in epilithic and epiphytic communities collected from spring to autumn.
Use of the rice sucrose synthase-1 promoter to direct phloem-specific expression of β-glucuronidase and snowdrop lectin genes in transgenic tobacco plants

The promoter region from the rice sucrose synthase-1 gene (RSs1) was fused with coding sequences for β-glucuronidase (GUS) and snowdrop (Galanthus nivalis) lectin (GNA). Tobacco plants were transformed with these chimaeric genes in order to determine the expression pattern directed by the RSs1 promoter. Histochemical and immunochemical assays demonstrated that the expression of both GUS and GNA was restricted to phloem tissue, and was not observed in any other tissues. This phloem-specific expression pattern was consistent in stem, leaf and root, and in different transgenic plants. Chimaeric genes of RSs1-GUS and RSs1-GNA were stably inherited in T1 plants
Myxobolus buri, the myxosporean parasite causing scoliosis of yellowtail, is synonymous with Myxobolus acanthogobii infecting the brain of the yellowfin goby

: Myxobolus buri Egusa, 1985, is a well-documented myxosporean parasite that causes the scoliosis of cultured yellowtail Seriola quinqueradiata. A similar parasite has been described as Myxobolus acanthogobii Hoshina, 1952, from the brain of the yellowfin goby Acanthogobius flavimanus, although this parasite is not associated with skeletal abnormalities in host fish. The present study aimed to re-examine the identification of these two parasites by morphological and molecular analyses. Morphological characteristics (e.g. presence of the intercapsular processes and several folds on the sutural ridges) and spore dimensions were not distinguishable between the two species and were consistent with those in the original descriptions. Molecular analysis indicated that small subunit rRNA gene sequences shared 100% identity between the two parasites. Consequently, it can be concluded that M. buri is synonymous with M. acanthogobii, and thus this parasite can be reassigned as M. acanthogobii.
Association of three begomoviruses and a betasatellite with leaf curl disease of basil in Oman

Abstract Basil (Ocimum basilicum) is an important medicinal and aromatic plant native to Asia and Africa. Among 30 different species of Ocimum, common basil is the most widely cultivated species in Oman. During a survey in A’Seeb, a wilayat of Muscat, Oman in 2014, disease symptoms such as severe leaf curling, yellowing, and crinkling were observed on basil plants. To confirm the potential association of begomovirus with this disease, symptomatic leaves were collected, nucleic acid was extracted, and rolling circle amplification (RCA) using Phi 29 DNA polymerase was performed. Restriction analysis of the amplified product was conducted and full-length clones of a putative begomovirus and betasatellite were isolated and characterized. Sequence analyses of several clones showed that the basil plants were infected with Tomato yellow leaf curl virus-Oman (TYLCV-OM), Chili leaf curl virus-Oman (ChLCV-OM), and Tomato leaf curl Albatinah virus (ToLCABV). Infected basil plants also harboured Tomato leaf curl betasatellite-Oman (ToLCB-OM), a satellite associated with leaf curl disease of tomato in Oman. All efforts to clone alphasatellites were unsuccessful, indicating that an alphasatellite was not associated with this infection. This is the first report of the association of multiple begomoviruses along with a betasatellite in the leaf curl disease of basil.
Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake

Bacterial diversity in the water column of a freshwater lake in the Netherlands was investigated by analysis of 16S rRNA gene sequences recovered through PCR amplification from total community DNA. Among 23 unique cloned sequences, two appeared to belong to the recently described bacterial division Verrucomicrobiales. One of the two sequences was most similar to a group of environmental clones that form a distinct lineage within the division. The other sequence was divergent (less than 85% similarity) from all 16S rRNA gene sequences, both from cultivated species and from environmental clones, known in this division to date. Analysis by denaturing gradient gel electrophoresis (DGGE) and sequencing of DNA recovered through excision from the DGGE gel showed that the two sequence types were present in the lake throughout the year.
Kinetics of Multivalent Antigen DNP-BSA Binding to IgE-FcεRI in Relationship to the Stimulated Tyrosine Phosphorylation of FcεRI

Multivalent DNP-BSA is commonly used to cross-link anti-DNP IgE bound to FcεRI to stimulate cellular responses, although key features of the binding process are unknown. Fluorescence quenching can be used to study the kinetics of DNP-BSA binding to FITC-IgE. We observe that DNP-BSA binds more slowly to IgE than does an equimolar amount of a monovalent DNP ligand, suggesting that the average effective number of DNP groups per BSA is less than one. The binding data are well described by a transient hapten exposure model in which most of the DNP groups are unavailable for binding but have some probability of becoming exposed and available for binding during the time of the binding measurement. Additional experiments indicate that, for suboptimal to optimal concentrations of DNP-BSA, most of the FITC fluorescence quenching on the cell surface is due to cross-linking events. With these concentrations at 15°C, the kinetics of FITC fluorescence quenching by DNP-BSA correlates with the kinetics of DNP-BSA-stimulated tyrosine phosphorylation of FcεRI. At 35°C, the phosphorylation kinetics are biphasic during the time period in which cross-linking continues to increase. Our results establish a quantitative relationship between the timecourse for cross-linking by multivalent Ag and FcεRI-mediated signaling, and they provide the means to predict the kinetics of cross-linking under a wide variety of conditions.
Hydrogen peroxide degradation by immobilized cells of alkaliphilic Bacillus halodurans

Whole cells of Bacillus halodurans LBK 261 were used as a source of catalase for degradation of hydrogen peroxide. The organism, B. halodurans grown at 55°C and pH 10, yielded a maximum catalase activity of 275 U g−1 (wet wt.) cells. The catalase in the whole cells was active over a broad range of pH with a maximum at pH 8–9. The enzyme was optimally active at 55°C, but had low stability above 40°C. The whole cell biocatalyst exhibited a Km of 6.6 mM for H2O2 and Vmax of 707 mM H2O2 min−1 g−1 wet wt. cells, and showed saturation kinetics at 50 mM H2O2. The cells were entrapped in calcium alginate and used for H2O2 degradation at pH 9 in batch and continuous mode. In the batch process, the immobilized preparation containing 1.5 g (wet wt.) cells could be recycled at least four times for complete degradation of the peroxide in 50 mL solution at 25°C. An excess of immobilized biocatalyst could be used in a continuous stirred tank reactor for an average of 9 days at temperatures upto 55°C, and in a packed bed reactor (PBR) for 5 days before the beads started to deform.
Four-dimensional carbon-13/carbon-13-edited nuclear Overhauser enhancement spectroscopy of a protein in solution: application to interleukin 1.beta.

A four-dimensional 13C/13C-edited NOESY experiment is described which dramatically improves the resolution of protein NMR spectra and enables the straightforward assignment of nuclear Overhauser effects involving aliphatic and/or aromatic protons in larger proteins. The experiment is demonstrated for uniformly (greater than 95%) 13C-labeled interleukin 1 beta, a protein of 153 residues and 17.4 kDa, which plays a key role in the immune response. NOEs between aliphatic and/or aromatic protons are first spread out into a third dimension by the 13C chemical shift of the carbon atom attached to the originating proton and subsequently into a fourth dimension by the 13C chemical shift of the carbon atom attached to the destination proton. Thus, each NOE cross peak is labeled by four chemical shifts. By this means, ambiguities in the assignment of NOEs that arise from chemical shift overlap and degeneracy are completely removed. Further, NOEs between protons with the same chemical shifts can readily be detected providing their attached carbon atoms have different 13C chemical shifts. The design of the pulse sequence requires special care to minimize the level of artifacts arising from undesired coherence transfer pathways, and in particular those associated with "diagonal" peaks which correspond to magnetization that has not been transferred from one proton to another. (ABSTRACT TRUNCATED AT 250 WORDS)
Techniques for Wildlife Habitat Management of Wetlands

A companion volume to "Techniques for Wildlife Habitat Management of Wetlands", this book provides an extensive compilation of techniques for habitat manipulation, which are designed to improve the biodiversity of uplands ecosystems for edge and interior game and nongame wildlife. It offers land managers, ecologists, and conservationists the latest structural and nonstructural methods for natural and cultural habitat improvements on forest lands, woodlots, rangelands, and farmlands. This practical manual includes expert discussions of guilds, minimum viable populations, edge vs. interior habitats, size of reserves and ecological succession, plus helpful guidance on how to alter plant succession for biodiversity by indirect and direct methods. This book should be a valuable tool in helping professionals maintain a healthy ecosystem and to restore or produce ideal populations of wildlife.
Introduction of a Cloned Gene into Fertilized Mouse Eggs and its Expression *

Abstract In order to analyze the role of enhancer sequence for the tissue‐specific and stage specific expression of immunoglobulin gene in normal diploid cells we have introduced cloned human y1 immunoglobulin genes into fertilized mouse eggs. Human y1 genes lacking enhancer sequence were not expressed in any tissues of transgenic mice. On the other hand human y1 genes containing enhancer sequence were expressed only in B lymphocytes. Levels of HIGI mRNA and percentage of human y chain producing cells in spleen cells were increased up to 50 times after treatment with lipopolysaccharide but not with Concanavalin A, suggesting B cell specific and regulated expression of HIGI gene. Human y chain producing cells were only found in the periphery of germinal center of the white pulp in histological section of the spleen suggesting stage‐specific expression. Human y chains appeared to be coupled with mouse light chains to form a complete IgG molecule and are secreted into cell supernatant. The production and secretion of endogenous immunoglobulin heavy and light chains in transgenic mice appeared to be the same as in normal mice. About one‐seventh of spleen cells that are producing endogenous mouse heavy chain produced human y1 chain at the same time. But no cell which produce only human y chain was observed. These results suggest that human γ chain expression had no effect on mouse immunoglobulin expression.
Interplay of Dengue Virus and the Human Immune Response

RIG-I is a key cytosolic sensor of many RNA viruses, including dengue virus (DV), the most significant arboviral pathogen. Upon viral RNA binding, RIG-I signals via the adaptor protein MAVS, located at mitochondria, to induce the expression of interferons (IFNs), proinflammatory cytokines and interferon-stimulated genes (ISGs), thereby establishing an antiviral state. Among the ISGs, the IFITM proteins are critical for antiviral restriction of numerous pathogenic viruses including DV by inhibiting viral entry. Here, we uncover how DV escapes RIG-I-mediated immunity. The NS3 protein of DV binds directly to 14-3-3ε, a mitochondrial-targeting protein that is essential for translocation of RIG-I from the cytosol to mitochondria. Specifically, NS3 blocks 14-3-3ε from forming a “translocon” complex with RIG-I and its upstream activator, TRIM25, thereby inhibiting RIG-I translocation to mitochondria for MAVS interaction and antiviral signaling. Furthermore, RIG-I that fails to translocate to mitochondria is degraded in a lysosome-dependent manner in DVinfected cells. Intriguingly, NS3 binds to 14-3-3ε using a phosphomimetic motif that resembles a canonical phospho-serine/threonine motif found in cellular 14-3-3-interaction partners. We engineer a recombinant DV encoding a mutant NS3 protein deficient in 14-3-3ε binding (DV2KIKP) and find that this mutant virus is attenuated in replication compared to the parental virus. Strikingly, DV2KIKP fails to antagonize RIG-I and elicits high levels of IFNs,
The quantitative assessment of arthropod predation rates by electrophoresis

SUMMARY The development of an electrophoretic technique for the quantitative assessment of specific prey material in the gut of a predator is described. Panonychus ulmi and Tetranychus urticae were used as test prey species. Samples prepared from these mites were electrophoresed on polyacrylamide concentration gradient slab gels, which were then treated to reveal esterase activity. The relationship of intensity of a stained band with sample concentration and staining time was not linear for some esterases. Possible causes of this non-linearity were identified but could not readily be eliminated. However, quantitative assessment of prey material is possible after the preparation of a calibration curve.
Absence of β-catenin Mutations in Mouse Hepatoblastomas Induced by N, N-dimethylformamide

Abnormal β-catenin protein accumulation in cytoplasm or nucleus with somatic mutation of β-catenin has been reported to be very frequent in hepatoblastomas (HBs) both in humans and in experimental animals. Recently we noted HBs developing in an evaluation of the carcinogenicity of N, N-dimethylformamide (DMF) in a 104 week mouse inhalation study1 performed by the Japan Bioassay Research Center. In the present study we evaluated β-catenin mutations in mouse HBs induced by DMF, which is considered to be a non-genotoxic carcinogen. Immunohistochemistry and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analyses were performed using formalin-fixed and paraffin-embedded sections. No abnormal β-catenin accumulation or no apparent mutation was detected, and these findings point to functional normality of the Wnt signal pathway in these HBs induced by DMF. Our results raise questions as to the general nature of any relationship between HB and abnormal β-catenin accumulation.
Characterization of a new virus from garlic (Allium sativum L.), garlic mite-borne mosaic virus

Flexuous, filamentous virus particles with a length of 700-800nm were detected in garlic (Allium sativum L.) plants showing mosaic symptoms. The virus was sap-transmissible from garlic plants to seven out of 25 plant species tested, inducing local lesions on Chenopodium morale and Gomphrena globosa and a systemic mosaic on garlic. This virus was transmitted by the eriophyid mite, Aceria tulipae Keifer, but not by aphids. Two polypeptides with MW. 30kDa and 28.5kDa were detected by SDS-PAGE of the purified virus preparation. The virus exhibited no serological relationships with leek yellow stripe, onion yellow dwarf or garlic latent viruses. No cytoplasmic cylindrical inclusions were observed in infected leaf cells of garlic or C. morale. The 3•Œ-terminal nucleotide sequence of 2518 by was determined. It contained three putative open reading frames (ORFs) for 40kDa, 28kDa (a putative coat protein, CP) and 15kDa polypeptides. The arrangement and amino acid sequences of these ORFs show close similarities with those of shallot virus X and garlic virus (GV)-A, -B, -C and -D. The putative CP of the mite-borne virus has 98% amino acid sequence homology with CP of GV-C, but only 60-67% identity with CPs of four other viruses, indicating the classification of the mite-borne virus and GV-C as the same virus. We propose the name garlic mite-borne mosaic virus (GMbMV) for the virus. (Received March 7, 1996; Accepted July 25, 1996)
Effect of mating on plasma juvenile hormone esterase activity in females of Choristoneura fumiferana and C. rosaceana.

We measured juvenile hormone esterase (JHE) activity in the plasma of virgin and mated Choristoneura fumiferana and C. rosaceana female moths. In these two species, JH III acid was the only measurable product of in vitro JH III degradation in the plasma. Rates of JH III ester hydrolysis were generally higher in C. rosaceana than in C. fumiferana, but followed a similar pattern in both species, with high activity measured on day 7 of the pupal stage, the lowest activity measured at emergence, and a subsequent increase observed between days 0 and 1. Mating on day 0, in both species, brought about a significant increase in JHE activity on day 1, relative to virgins. On days 3 and 5, rates of JH degradation did not differ between virgin and mated females. The mating-induced increase in JHE activity on day 1 was not the result of a decrease in blood volume in mated females relative to virgins. Fluctuations in JHE activity did not appear to depend on changes in plasma protein concentration. In both species, topical application of JH I or methoprene, on the day of emergence, resulted in dose- and time-dependent increases in JHE activity relative to controls. © 1996 Wiley-Liss, Inc.