Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of combined thermophilic composting and vermicomposting on biodegradation and sanitization of mixtures of dairy manure and waste paper

Thermophilic composting is commonly used for the treatment of organic wastes or for production of organic/natural fertilizers. Vermicomposting (V) is also increasingly becoming popular. These two techniques have their inherent advantages and disadvantages. In this study, vermicomposting and a combination of thermophilic composting and vermicomposting were compared as ways of sanitizing and biodegrading dairy manure and waste paper mixtures with C:N ratios of 30 and 45. Wastes with a C:N ratio of 30 proved more suitable for both vermicomposting and combined thermophilic composting and vermicomposting as their composts were more stabilized and with higher nutrient contents than composts made from wastes with a C:N ratio of 45. Both vermicomposting and combined composting and vermicomposting were effective methods for the biodegradation of dairy manure and paper waste mixtures with C:N ratio of 30 but the latter was more effective in the biodegradation of waste mixtures with a C:N ratio of 45. Combining therrmophilic composting and vermicomposting eliminated the indicator pathogen Escherichia coli 0157 from the final composts whereas vermicomposting only managed to reduce the pathogen population.
Characterization of TEM-Mediated Ampicillin Resistance in Salmonella typhi Isolates of Pakistan

Typhoid fever or Salmonellosis is a systemic disease caused by the Gram-negative pathogen Salmonella typhi. It is still a serious problem in most of the third world countries. Many antibacterial drugs are being used for its treatment, but emergence of drug-resistant strains has prompted scientists worldwide to opt for an alternative approach. For this reason, we characterized the resistant strains, so as to determine their pattern of resistance to antibiotics. Fifty seven (57) multidrug-resistant (MDR) S. typhi were isolated from 200 blood samples obtained from patients with typhoid fever. Minimum Inhibitory Concentration (MIC) was determined against Ampicillin, Sulfamethoxazole, Ofloxacin, Chloramphenicol and Streptomycin. Plasmid profiling was done and analyzed by gel electrophoresis. PCR of 848 bp region in TEM gene was performed to check the presence of Extended Spectrum 􀀁-Lactamase (ESBL) gene. Five out of nine (55.6%) isolates were found positive for ESBL. Research for characterizing ESBL isolates in different pathogenic bacteria is going on globally. This character cannot only be transferred to other bacteria through conjugation, but also using conventional drugs may lead to the development of new resistant strains.
Cloning and Expression Analysis of Two Endo-1,4-β- Xylanase Genes from Phanerochaete chrysosporium

The complete sequence analysis of two β-1,4-xylanase genes, xynA and xynB, from the model lignocellulose degrading white rot fungus Phanerochaete chrysosporium to the GenBank database (accession number AF301902 to AF301905 has been reported. Here we report the cloning and the successful expression of both genes to significant levels in a pET-based E. coli expression system. The size of the expressed proteins, XYNA and XYNB were approximately 48 and 37 kDa, respectively. In both cases, the vast majority of the expressed protein was located in the insoluble fraction presumably within the inclusion bodies. Finally, the presence of the recombinant proteins was confirmed by Western Blot analysis.
Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes

Potato fields in the Central Andean Highlands are mostly owned by small farming communities that are settled in remote areas, free of intense anthropogenic influences. These communities grow potatoes because they provide cheap but nutritious foods to the farmers. The biggest share of grown potatoes is used for consumption by the communities; only a small proportion is meant for export. These farming communities are often poor, and largely depend on crop yields. Crop diseases are disastrous and as a result, local farmers are willing to put their fields at microbiologists’ disposal for studying disease protection programs.
Methylene blue reduction test in semen analysis of White Pekin ducks

This study was undertaken to investigate the relationship between methylene-blue reduction time (MBRT) and other semen quality parameters in duck by analysis of correlation coefficients. Semen ejaculates (32), collected at 2 days interval from 10 randomly selected drakes, were examined for different seminal parameters like pH, volume, colour, mass activity, individual motility, livability, concentration, number of spermatozoa per ejaculate, total sperm abnormality per cent and MBRT. The overall mean time to decolourise methylene blue in the white Pekin ducks was 10.03±0.24 min with a range from 8 to 13 min. MBRT was negatively correlated with mean spermatozoa concentration, number of spermatozoa per ejaculation and colour of semen samples but positively correlated with individual motility and livability. High correlation of MBRT with seminal parameters indicated its practical utility in monitoring semen characteristics.
A taxonomic study on Gyrodinium aureolum HULBURT (Dinophyceae) from the morphological viewpoint based on materials collected in Japanese coastal waters

~ nt~~~~! WJ¥ff~~Gy rodinium aureolum T 852 *~mX~PlJl-143) ***¥7~7~~~~~~W~~ /~­ Abstract: For unarmored dinoflagellates which includes harmful species, observation of fragile morphology is indispensable in arriving at correct biological names. However, the difficulties in fix­ ation and preservation of detailed characteristics brings about coufusion due to unstable taxonomic decision. This leads to the creation of new synonymous species name or innocent misuse of known species name. Repetition of this practice increases difficulty in species identification. Gymnodinium mikimotoi Miyake et Kominami ex Oda (abbreviated as Gym. mikimotol) and Gy­ rodinium aureolum Hulburt (Gyr. aureolum) are two major harmful unarmored species reported in several countries and these species are in state of taxonomic confusion. In Japan, Gym. mikimotoi is considered most noxious and had devastated the fishing and aquaculture industries since 1960's. In northern Europe, another unarmored species called either Gyr. aureolum or Gymnodinum sp. cf. mikimotoi is known to cause serious damages in coastal waters. Morphological similarities between these species have cause taxonomic confusion for the last two decades. This study was conducted to clarify the taxonomic problems by observation of materials collected from Japanese waters and re-interpretation of original and succeeding morphological descriptions. After careful LM and SEM observation of the two species which occurred simultaneously in the coastal waters of Tanabe Bay, central Japan, and literature survey of these species, we concluded the separation of the two species should be based on the the following morphological characteris­ tics and behavior.
CRANIAL ANATOMY AND TAXONOMY OF THE LATE PERMIAN DICYNODONT DIICTODON

ABSTRACT Reexamination of the cranial anatomy of the abundant Late Permian dicynodont Diictodon confirms suggestions that only one species, D. feliceps, is recognizable. This monotypic genus is highly distinctive, being characterized by such features as a palatal notch, a large dentary table with a medial cutting blade, and the absence of postcanine teeth. Numerous anatomical variations exist within D. feliceps, but many appear biologically insignificant and show no apparent correlation with one another of with locality or stratigraphic position. However, statistical analysis reveals the presence of several features that correlate with the presence of canine tusks, including an occipitally positioned postparietal bone and the presence of a boss surrounding the pineal opening. This suggests that tusked and tuskless specimens do indeed represent distinct biological categories, but it seems highly probable that they are divisions within a single species (most probably opposite sexes) rather than distinct species. It is hoped that the detailed osteological description of the Diictodon skull presented here will provide useful data for future phylogenetic analyses of dicynodonts.
Revision of the genus Atychodea Reitter with a Consideration of the Relationships in the tribe Tychini (Coleoptera, Staphylinidae, Pselaphinae)1

Abstract Atychodea Reitter is re-described, and descriptions of the eight species included are given. Three of these were known and have been included in this genus earlier, two, from other genera, newly included in Atychodea, and three are new (A. portentosa sp. n. from Myanmar, and A. fedorenkoi sp. n. and A. vicina sp. n. from southern Vietnam). One species, A. lenticornis Reitter, is excluded from this genus and a new monotypic genus Amorphodea gen. n. is described to include this species. A key to the species of Atychodea is given. On the basis of a large set of morphological data, the relationships of all genera of the Tychini are considered, and Hesperotychus Schuster and Marsh and Tychomorphus Jeannel are synonymized with the genus Tychus Leach. A key to genera of Tychini is given. A complete catalogue of the tribe, with 20 new combinations and 12 revised combinations, with data on species distribution, is also provided.
First record of the sea anemone Anthopleura nigrescens (Cnidaria: Actiniaria: Actiniidae) on the Pacific coast of Central America

f.h. acun~a, j. alvarado, a. garese and j. corte’s Instituto de Investigaciones Marinas y Costeras, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250, 7600 Mar del Plata, Argentina, Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, Costa Rica, Centro de Investigación en Ciencias del Mar y Limnologı́a (CIMAR), Ciudad de la Investigación, Universidad de Costa Rica, San Pedro, 11501–2060 San José, Costa Rica, Escuela de Biologı́a, Universidad de Costa Rica, San Pedro, 11501–2060 San José, Costa Rica
The species pool concept as a framework for studying patterns of plant diversity

Co-existence theories fail to adequately explain observed community patterns (diversity and composition) because they mainly address local extinctions. For a more complete understanding, the regional processes responsible for species formation and geographic dispersal should also be considered. The species pool concept holds that local variation in community patterns is dependent primarily on the availability of species, which is driven by historical diversification and dispersal at continental and landscape scales. However, empirical evidence of historical effects is limited. This slow progress can be attributed to methodological difficulties in determining the characteristics of historical species pools and how they contributed to diversity patterns in contemporary landscapes. A role of landscape-scale dispersal limitation in determining local community patterns has been demonstrated by numerous seed addition experiments. However, disentangling general patterns of dispersal limitation in communities still requires attention. Distinguishing habitat-specific species pools can help to meet both applied and theoretical challenges. In conservation biology, the use of absolute richness may be uninformative because the size of species pools varies between habitats. For characterizing the dynamic state of individual communities, biodiversity relative to species pools provides a balanced way of assessing communities in different habitats. Information about species pools may also be useful when studying community assembly rules, because it enables a possible mechanism of trait convergence (habitat filtering) to be explicitly assessed. Empirical study of the role of historic effects and dispersal on local community patterns has often been restricted due to methodological difficulties in determining habitat-specific species pools. However, accumulating distributional, ecological and phylogenetic information, as well as use of appropriate model systems (e.g. archipelagos with known biogeographic histories) will allow the species pool concept to be applied effectively in future research.
HALOSTYLODINIUM ARENARIUM, GEN ET SP. NOV. (DINOPHYCEAE), A COCCOID SAND‐DWELLING DINOFLAGELLATE FROM SUBTROPICAL JAPAN

A new genus and species of marine coccoid dinoflagellate from subtropical Japan, Halostylodinium arenarium Horiguchi et Yoshizawa‐Ebata, gen. et sp. nov., is described. The dominant stage of the dinoflagellate is a nonmotile ovoidal to spheroidal cell with a distinct stalk. The stalk consists of an upper thick tubule, a lower thin tubule, and a discoidal holdfast. The dinoflagellate possesses a yellowish‐brown chloroplast with multiple lobes radiating from a central pyrenoid. It reproduces by the formation of two motile cells, which swim for a short period and then transform directly into the stalked nonmotile cell. The stalk is produced during transformation from the apical stalk complex present in the apex of the motile cell. The apical stalk complex consists of a double‐folded apical pore plate and doughnut‐shaped holdfast‐building material. The ultrastructure of the apical stalk complex is compared with those of Bysmatrum arenicola and Stylodinium littorale. Halostylodinium arenarium possesses delicate thecal plates, and the thecal plate formula is Po, 5′, 2a, 7″, 7c, 6s, 5″′, 1p, 2″″. A phylogenetic study based on the 18S ribosomal RNA gene did not show any clear affinities between this organism and any species included in the analysis.
BREEDING FOR SALT-RESISTANCE USING TRANSGRESSIVE SEGREGATION IN SPRING WHEAT

Hybrid populations (F3) derived from cross between four moderate saltresistant spring wheat (Triticum aestivum L.) were assessed for transgressive segregation of salt-tolerant genotypes allowing germination and emergence at 350 mM NaCl for 30 days. The achieved Selection intensity was the order of 0.240. 27 in these segregation populations (22-25 seedlings from 9000 seeds). Assessment of transgrassive individuals (more salt tolerant) and their parents was carried out in a hydroponics experiment applying six salt concentrations of 150, 200, 225, 250, 275 and 300 Mm NaCl. Root lengths of two-week-old seedlings grown in the different concentrations were used as salt-tolerant criteria. Root length of transgressive plants were longer than parents (except Tobari 66) showing more tolerance to NaCl. It may be assumed that the character in quantitative trait based, and the parents of such hybrids may contain different genes for salt tolerance.
Technology Review: Molecular Approaches for Quantifying DNA Synthesis and Cell Proliferation During Rodent Bioassays

The induction of sustained, chemically-induced regenerative hyperplasia during rodent bioassays may result in carcinogenesis. Hence, accurate measurement of replicative DNA synthesis and cell proliferation in putative target organs during acute and subchronic assays will aid in dose selection for chronic studies; and assessment of cell proliferation rates during chronic bioassays will aid in the interpretation of results and in risk assessment. Histopathology is the traditional method for assessing hyperplasia and will continue to be of paramount importance. However, quantitative molecular approaches for assessing rates of DNA synthesis and mitogenesis in many cases extend and complement histopathological examinations. Three of these methodologies, incorporation of radiolabeled thymidine into DNA, incorporation of bromodeoxyuridine into DNA, and measurement of proliferating cell nuclear antigen, are discussed in this review. Also, a relatively new technology, the use of flow cytometry to measure the incor.
Fetal Alveolar Epithelial Cells Contain [d-Ala2]-Deltorphin I-like Immunoreactivity

Opiate-like peptides can regulate many cellular functions. We now map [d-Ala2]deltorphin I (DADTI)–like immunoreactivity (DADTI-LI) in developing mouse lung and analyze potential functional roles. Most DADTI-LI–positive cells were alveolar cells negative for prosurfactant protein (proSP)-C immunoreactivity. Peak numbers of DADTI-LI–positive cells occurred on embryonic Day 18, decreasing postnatally. To analyze developmental effects of DADTI, e17-18 lung explants were treated with [d-Ala2]deltorphin II (DADTII, soluble DADTI analogue, δ -receptor–specific) versus dermorphin ( μ -receptor–specific). Type II pneumocyte differentiation, assessed by [3H]choline incorporation into saturated phosphatidylcholine and proSP-C immunostaining, was inhibited by DADTII but stimulated by dermorphin. Cell proliferation, measured as [3H]-thymidine incorporation and proliferating cell nuclear antigen immunostaining, was stimulated by DADTII and inhibited by dermorphin. All effects were dose-dependent. DADTII-inhibited chol.
Impacts of seagrass habitat architecture on bivalve settlement

We investigated the effects of differing spatial scales of seagrass habitat architecture on the composition and abundance of settling bivalves in a sub-tropical seagrass community. The density of newly settled bivalves was generally greater atThalassia testudinum grass bed edge (<1 m) compared to interior portions of the bed (>10 m). Deviation from this generalized pattern occurred when high densities of newly settled tulip mussels (Modiolus americanus) were recorded from the interior of the meadow, associated with aggregations of adult mussels. Bivalve settling densities appear to reflect settlement shadows of passively delivered larvae, bedload transport of newly settled individuals from unvegetated regions, as well as gregarious settlement among adult conspecifics. We also investigated the impact of seagrass patch shape and size on settlement by using artificial seagrass units (ASU) in separate short-term and long-term experiments. We found a positive relationship between ASU perimeter and bivalve abundance, suggesting that larval encounter rates with seagrass habitat may determine initial settlement patterns. Using ASUs we also investigated the relative role seagrass epiphytes play in determining the density of settling bivalves. Results showed greater settling densities where epiphytic secondary structure was elevated compared to controls, and bivalve density was significantly greater when ASUs were fouled with a natural community of epiphytes, suggesting that both microstructure and biofilms positively influenced bivalve settlement. We conclude that structural components of seagrass habitats increase bivalve settlement at multiple spatial scales, including epiphytic micro-structure, small-scale patch shape and size, and large-scale within habitat differences.
Review on Phytochemical Study of Asteraceae in Taiwan (1996~2005)

Asteraceae is the third largest family (next to Orchidaceae and Poaceae) of flowering plants in Taiwan. Two hundred twenty-one species and 20 additional infraspecific taxa in 84 genera were recorded in the 2nd edition of Flora of Taiwan (1998). About 74 species in 51 genera have been used in folk medicine, and 30 species in 22 genera have been studied chemically. The diversity and complexity of the chemical constituents in these plants are enormous. Various natural products such as terpenes, flavonoids, coumarins, alkaloids, polyalkynes, etc. have been found. Among them, sesquiterpenes and polyalkynes are often species-specific. Folk medicine of Asteraceae used in Taiwan is claimed to have the properties of antipyretic, detoxication, antibacterial, antiphlogistic, hypotention, blood stasis removal, hemostasis, expectoration, cough-relieving, and most importantly, antihepatitis and antitumor. Prior to 1990, the majority of studies on Asteraceae in Taiwan focused on chemical analysis. In vitro studies using selected cells or cell line to screen the activities of crude extracts were the theme in the 1990s. More recently, pure compounds were isolated and studied in relation to their action mechanisms. Due to lots of plants of this family are commomly used as folk medicine. Review articles have already appeared on the natural product research in Taiwan before 1996. This present review deals with the plants of Asteraceae which have been investigated in Taiwan during 1996 to 2005.
GENE AND ENZYMATIC ACTIVITIES OF ARABIDOPSIS D-AMINO ACID OXIDASE IN SALTY MEDIA

Summary: The relative gene expression and the enzymatic activity of D-amino acid oxidase (DAAO) were assessed in the leaves of Arabidopsis plants grown under salt stress and a subsequent recovery period. Analysis of the distribution patterns of the gene expression by using semi-quantitative and real-time reverse transcription and polymerase chain reactions (RT-PCR) revealed that daao gene was inducible in the leaves of the test plants under salty growth medium. The distribution patterns of DAAO enzyme activity towards D-aspartate, D-alanine and D-serine showed that D-aspartate oxidase was more likely an inducible DAAO enzyme in salt-challenged test plants. Parallel experiments related to antioxidant abilities provided further assessment criteria for clarification of a potent resistance mechanism. It was indicated for the first time that D-aspartate oxidase might be a DAAO of pivotal importance for salt-challenged Arabidopsis plants, proposing a DAAO-dependent strategy as a new candidate and promising target for salt resistance engineering in plant systems. Citation: Gholizadeh A. , 2013. Gene and enzymatic activities of Arabidopsis D-amino acid oxidase in salty media. Genetics and Plant Physiology, 3(3–4): 133–145.
Hypoxia-Induced Gene Expression Occurs Solely through the Action of Hypoxia-Inducible Factor 1α (HIF-1α): Role of Cytoplasmic Trapping of HIF-2α

ABSTRACT The hypoxia-inducible factors 1α (HIF-1α) and 2α (HIF-2α) have extensive structural homology and have been identified as key transcription factors responsible for gene expression in response to hypoxia. They play critical roles not only in normal development, but also in tumor progression. Here we report on the differential regulation of protein expression and transcriptional activity of HIF-1α and -2α by hypoxia in immortalized mouse embryo fibroblasts (MEFs). We show that oxygen-dependent protein degradation is restricted to HIF-1α, as HIF-2α protein is detected in MEFs regardless of oxygenation and is localized primarily to the cytoplasm. Endogenous HIF-2α remained transcriptionally inactive under hypoxic conditions; however, ectopically overexpressed HIF-2α translocated into the nucleus and could stimulate expression of hypoxia-inducible genes. We show that the factor inhibiting HIF-1 can selectively inhibit the transcriptional activity of HIF-1α but has no effect on HIF-2α-mediated transcription in MEFs. We propose that HIF-2α is not a redundant transcription factor of HIF-1α for hypoxia-induced gene expression and show evidence that there is a cell type-specific modulator(s) that enables selective activation of HIF-1α but not HIF-2α in response to low-oxygen stress.